The owners' taking a salary isn't really an issue. I believe the poster who brought it up did so as an (unlikely) example of how easy it is to disguise profit by trumping up expenses. A more likely scenario involves owners giving sweetheart deals to their other business holdings, like, say, Kraft overpaying the real estate arm of his holding group for the land for Patriot Place. The NFL Network is a huge source of potential odd accounting arrangements -- are teams getting full compensation for any stadium licensing rights they retain from the house network?
Essentially, what this comes down to, is that the NFL is trying to justify asking for the players to take a collective billion-dollar pay-cut by saying that under the previous CBA, their decline in profitability hurt their ability to reinvest in the growth of of their franchises and the NFL -- and they're asking the NFLPA to take their word that it's necessary.
The problem is that the owners can't agree on how much more information to provide. I'd imagine that Kraft would readily hand over his books -- considering the way he's grown the NE Patriots from one of the league's least valuable teams to one of its most, he probably carries around his financial statements in his wallet the way a guy would pictures of his supermodel girlfriend or a big fish he caught. It's the teams like the Browns, Bengals, Bills, Niners, Lions, etc. who haven't done much to maximize other revenue streams that are dragging collective profitability numbers down who don't want the teams' books released, because it will become apparent that they haven't been attempting to reinvest in the growth of their franchises since long before the last CBA was signed.
Essentially, what you have are deadbeat owners who want a handout from the league to do what the Snyders, Krafts, Jones and Johnsons have been doing all along, and the non-deadbeat owners don't want to pony it up by bringing more revenue streams into the profit sharing system, so instead, the owners, collectively, are trying to head off internal arguments by getting the money back from the players.