If you can identify the source(s) of the discrepancies from prior year returns, you may adjust the current year return to report the beginning balance as it should be. Ideally, you would amend the prior year returns to correct Schedule M-2, but often that is not worth the effort. Retain your workpapers to document how you adjusted the balance, both for your records and in case the IRS has questions (unlikely).
Since you have nearly completed the S-Corp return, you should stick with it until you can e-file. Next year, buy the desktop software so you have more control and access to the forms.
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