One of the issues that got swept aside during the agency pricing discussions was "why did Random House hold out for traditional pricing?" There was some speculation that it was to keep authors in the dark:

I agree, but don’t think Random is afraid of lower prices. Instead, like many publishers, the company fears that clear sales numbers might give authors access to information they’re not supposed to see.
...
For the most part, the transactions are clear and the exchange of money straightforward to follow. A publisher sells a given number of copies and gets a fixed percentage of list price for each. Forget reserves, confusing discount levels, and effectively dropping author royalties. There is no way to obfuscate the business details, and authors can demand what they should make, rather than have complexities and “mistakes” that leave authors poorer and a publisher richer.

Of course, there's always the option of "just LIE on the royalty statements." (And like she says, I think malice is less likely than "we don't want to pay thousands of dollars and change our whole accounting system to deal with all this new weird information.")

I hope the discrepancies are enough to get a subpoena for accurate numbers, perhaps directly from Amazon & B&N. A really cool long-term outcome would be authors having the right to demand their sales numbers directly from the ebook stores... after all, it can't be too much of a hardship to email a sales report to an additional person. (I know, is more complicated than that. Publishers may get numbers for all their authors combined in a single report. But I know Amazon can run single-title reports; they do it for indie authors.)