An End to Days of High Cotton? (washingtonpost.com): "Despite the limits, for example, Colorado River Indian Tribes Farm of Parker, Ariz., collected $2.4 million in payments in 2003 related mainly to cotton production, and Perthshire Farms, a huge Mississippi cotton operation, took in $2.1 million, according to the Environmental Working Group, an advocacy organization that publishes and analyzes USDA data."
My guess is that the first operation is an Indian tribal venture, which, if memory serves (current rules may differ), were treated almost as if exempt from payment limitation. Remember that, except when forced by the government, Indians "owned" land in common, not as separate parcels. So modern Indian farmers might well want to farm together in a tribal venture using their commonly owned land. Assume there were 50 farmers in the venture and the limitation was $100,000 (for ease of calculation). Each, if farming individually, could receive up to $100K in payments (if otherwise earned). Because the 50 are farming together as a venture, we treated the venture as if it had a limitation of $5 million (50 x $100K) .
The Mississippi operation may be a "Mississippi Christmas tree"--that is an operation carefully constructed by lawyers to evade the limitation rules. The NY Times did a series on them in 1990 or so, but they've had the political clout (think Sen. Lott) to keep the rules from being changed.