Thanks for the reply. We solved the problem as well, and it was caused by a similar reason. Each time we exercised our RSUs (once a quarter), two transactions occurred. One set of stocks were traded "for tax purposes" and another set for cash which we actually received. So when filling out the survey, we used the total of both, and marked the first set as "withheld". That was bad.
While those WERE withheld, they had already been accounted for in the W2. They were relevant only for the (very short) period between vesting and trading. It's the gain/loss of that time period that we're entering, so the solution was just to treat all transaction as standard 1099-B entries with no withholding.
The error we experienced didn't lead us in that direction at all, so hopefully if you found this via google it was helpful.
