I am finding discrepancies between Tax Return and Books when using TT for Business when I get to the Reconciliation of my Balance Sheet and Retained Earnings. I imported my QB data into Turbotax and had a $4 difference in my Balance Sheet between TT and QB. Now I have a larger ($600) difference in my retained earnings between Books and Tax Return.
I assume that there are entries in QB that didn't get mapped to TT, but not really sure of how to go about finding these or if it's an entirely different problem.
Have you looked at your balance sheet in Forms Mode with TurboTax Business?
I am not familiar with QuickBooks but if there is something similar, you should be able to compare the two.
Update: It appears that TT doesn't enter in non deductible expenses like tax penalties and interest from QB. As a result, if you don't manually enter them in the forms (M1 worksheet), your Retained Earnings will not balance in TT. You have to be careful though, as TT can remove the manual forms entry if you walk through the Balance Sheet reconciliation again.