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So it seemed last week as lawmakers sent the White House an updated budget for the Agriculture Department complete with industry-backed orders on how Secretary Tom Vilsack should run the place.

The Post-it notes from the packers were hard to miss.

Alarmed that automatic spending cuts this month will slow plant operations, the meat lobby won a last-minute Senate amendment that cuts from a new White House-backed school breakfast program in order to ensure there will be enough money to keep food safety inspectors on the job this summer and avoid disruptions.

At the same time the industry went in the opposite direction, denying funds in the Ag budget for implementing reforms sought in the 2008 farm bill to provide greater protection for less powerful ranchers and farmers who raise the animals for slaughter.

Money is again denied to proceed with rules favored by Western cow-calf operations in their battle with beef packers. In the case of poultry, the bill goes a big step further, literally ordering Vilsack in 60 days to rescind regulations adopted last year to protect growers under contract with the big chicken processors.

Even the typically conservative American Farm Bureau opposed this last action. And proponents would argue that the doomed poultry rules were never more than minimal protections for growers, such as requiring 90-day notice before a contract is cancelled by a packer.

“It’s almost as if the poultry companies are sending the signal through Congress: ”’you can’t touch us,’” said Steve Etka, who represents a coalition of growers.

“It doesn’t get much lower than that,” said Mike Weaver, a 61-year-old West Virginia chicken farmer. “They should all be ashamed. Anyone who could do that doesn’t have much integrity or soul.”

The orders to Vilsack on genetically-modified seeds are more subtle but potentially far reaching.

In no uncertain terms, the amendment tells the secretary how he must respond the next time a court order challenges one of Monsanto’s genetically-modified seeds for which the St. Louis-based giant is a pioneer in commercializing.

The real life impact is unclear as the underlying spending bill expires Sept. 30. But Monsanto gets a foot in the door toward mandating some type of stewardship program under which farmers can continue to plant its seeds as the court fight continues.

The language is unusually strong: the secretary “shall, notwithstanding any other provision of law… immediately grant” temporary permits to continue using the seed at the request of a farmer or producer wanting such a stewardship program.

Monsanto’s lobbying papers say the goal is to allow “continued cultivation in the interim period” subject to protections that “fairly balance any environmental concerns with the needs of the farmers.” In this regard, proponents argue that the proposal is consistent with what some courts have done themselves in the past, and Monsanto successfully expanded support among farm groups looking for greater certainty as well.

Nonetheless the sweeping mandate exposes the company to the charge of “court-stripping.”

The Center for Food Safety, a Washington-based non-profit which has been waging its own guerrilla war with the biotech industry, denounced the Monsanto measure as “corporate welfare” and a backroom deal. “Monsanto flexed its muscle and won,” said attorney Bill Snapes, who serves as counsel to the Arizona-based Center for Biological Diversity.

Vilsack’s own reaction suggests he has doubts about the amendment’s legal standing.

“Secretary Vilsack has asked the Office of General Council to review this provision,” the department told POLITICO, “As it appears to preempt judicial review of a deregulatory action which may make the provision unenforceable.”

Yet for all the anger — and belated legal reviews — no one can truly be surprised by the packers’ success nor Monsanto’s. Indeed the collapse of the traditional appropriations process in Congress may magnify the power of single-interest lobbies which have the money and skill to stay focused on their goals.

Both the packer and Monsanto provisions are virtually identical to what was publicly aired last summer by the Republican-controlled House Appropriations Committee in its initial fiscal 2013 bill to fund USDA. What’s really new is that measure never made to the House floor — nor did the Senate act on its own 2013 appropriations bill for the department.

Instead a House-Senate compromise of the draft bills was brokered in December to include the House language. It was this package which was then folded into the continuing resolution or CR sent onto President Barack Obama last week for his signature.

All this happened with little or no floor debate and in a period of turmoil for the Senate Appropriations Committee.

Sen. Herb Kohl (D-Wis.), who had resisted such House-riders in the past as chairman of the appropriations subcommittee responsible for the Ag budget, retired from the Senate at the end of last year. The chairman of the full Senate committee, Sen. Daniel Inouye (D-Hawaii) died shortly before Christmas.

On balance, these changes tipped the balance even more toward the National Chicken Council, representing the big poultry processors.

Sen. Mark Pryor (D-Ark.), who took over the Ag spot from Kohl, hails from the home state of Tyson Foods, headquartered in Springdale. Perdue Farms, a second big council member, has deep roots on Maryland’s Eastern Shore represents by Sen. Barbara Mikulski (D-Md.) who succeeded Inouye as chairman.

But the biggest player may have been Sen. Roy Blunt (R-Mo.), a battle-scarred veteran of the House GOP leadership who is now rebuilding his power base in the Senate.

Coming from Missouri, Blunt is a strong ally for both the poultry companies and Monsanto, and as the ranking Republican on the Ag appropriations subcommittee, he was a consistent and determined presence.

“Well, it’s in there and it works,” Blunt laughed, when asked about rescinding the poultry rules. “Everybody knew it was going to be permanent,” Blunt told POLITICO. “This is no ‘the House and Senate didn’t know what the House and Senate were doing.’ We accepted it in December.”

In the case of the Monsanto rider, Blunt said he worked with the company and had a valuable partner in the late chairman, Inouye, who was sympathetic given Monsanto’s large seed operations in Hawaii.

“What it says is if you plant a crop that is legal to plant when you plant it, you get to harvest it,” Blunt said. “But it is only a one year protection in that bill.”

Having helped secure both riders, Blunt moved next to work with Pryor to get the extra money their meat packer allies wanted to protect the industry against threatened furloughs at the Food Safety and Inspection Service. The March 1 automatic cuts took more than $50 million from FSIS’s appropriation; the bill now restores about $21 million of this reduction.

Pryor, faced with a tough re-election campaign in Arkansas, was someone Senate Majority Leader Harry Reid (D-Nev.) was inclined to help in any case. But Blunt also ingratiated himself with Reid and the Appropriations Committee leadership by supporting cloture on the underlying bill — even before the meat amendment was assured of a vote.

As the new appropriations subcommittee chairman for Ag funding — and a former state attorney general who prided himself on standing up for consumers — Pryor insisted that he had had little say about the Monsanto and packer riders Blunt and the House put in that title of the larger CR.

“We really didn’t modify anything that they did,” he said. But Pryor said he had felt obliged to intercede in the case of FSIS funding because of the direct impact on plant operations — including those in his home state.

“Unlike a lot of things in sequestration that had an immediate and direct impact on the private sector,” Pryor said. “A one to one ratio: if a meat inspector got furloughed that plant had to basically get furloughed for the day.”

Watching the bill with dismay was Sen. Jon Tester, a 56-year-old Montana Democrat and one of the few farmers in Congress.

In his lifetime, Tester has witnessed first-hand the immense consolidation of power at the top of the meat industry and was one of those in Congress who urged the Ag department to be more aggressive with its regulatory power under the 1921 Packers and Stockyards Act. At the same time, as an organic farmer himself, Tester is leery of the power enjoyed by Monsanto and the introduction of new GMO (genetically modified organism) products tailored to work better with herbicides.

Tester’s background and Western roots encapsulate many of the tensions today in agriculture itself.

On one side are the arguments for greater efficiency in the production of food — something the big meat packers would say they provide — even at the expense of smaller ranchers. In the case of Monsanto and the new GMO frontier, Vilsack himself has championed science that can improve production to feed the world’s expanding population.

“With the seed genetics today that we’re seeing,” he enthusiastically told the Chamber of Commerce in December, “Miracles are occurring every single growing season.”

On the other side is a fear — shared by many in agriculture — that some measure of fairness and safety is being lost in the process.

Thus while the Chicken Council celebrated last week — “We’re grateful that both the House and Senate showed strong support for these provisions” — Vilsack’s response was not happy.

“It is unacceptable that Congress has once again stepped in and decided to further reduce basic protections for poultry producers,” his office said. “USDA will continue to look for ways including appropriate enforcement of existing protections to provide greater fairness and transparency in the marketplace for our nation’s farmers and ranchers.”

Tester waited too long to be a major force, and critics would argue that as a member of the Appropriations panel, he should have seen the train coming at him sooner. But he did file amendments – which were never allowed votes — to strip out both the riders. In private, he made his displeasure known to top Appropriations Committee staff, and he delivered a strongly-worded floor speech likening the provisions to essentially earmarks for industry.

“We’re back to square one with the big meatpackers calling the shots,” Tester told his colleagues.

“These provisions are giveaways, pure and simple, and will be a boon worth millions of dollars to a handful of the biggest corporations in this country,” Tester said. “They deserve no place in this bill. We simply have got to do better on both policy and process.”