The increase in shareholder loan and APIC doesn't affect the AAA at all, they only affect the shareholder's basis. To be sure that I'm completely in balance, I always opened the "Options" tab in the 1120S form of ATX and checked the box to force completion of the balance sheet and M-1 so that I could view it on the screen, do my final review, sometimes would print pg 4 of the 1120S for my file, and then uncheck the box before filing. Unless you are keeping the books on the tax basis of accounting and not GAAP, it is entirely possible, and not even unusual, to have a different AAA for tax than AAA per books because of temporary timing differences. Those are the same as for C corps (tax vs book deprec, bad debts, acc'd shareholder distribs, sec 263 inventory adjustments, accr'd shareholder salaries, accr'd vacation pay, cap lease amort and interest, rent adjustment under sec 267, and accumulated timing diffs from prior years that haven't yet reversed. Permanent differences arising from nontaxable income and nondeductible expenses are on Sch K and flow through to M-1 and M-2, and these do not cause differences in the AAA and retained earnings. Joan, I think you are missing that ATX does have a worksheet to record the timing differences, if any, because ATX does allow for this. If you click on a line in the balance sheet on pg 4 it takes you to the balance sheet input. On that screen, you will note that the ending retained earnings line is white and doesn't allow for input, but it has an arrow that will "jump" to another worksheet where these timing differences can be entered. I hope this helps, and I hope you are really in balance at this point, but your statements about the change in shareholder loan and APIC have me wondering.