Unrealized Gains on Balance Sheet

First of all, ensure that you even have to complete Schedule L. 

You do not have to complete Schedule L if the S corporation's total receipts were less than $250,000 for the tax year, and the corporation’s total assets were less than $250,000 at the end of the tax year.

Otherwise, your scenario may be unique and require an entry in Liabilities and Equity, specifically Adjustments to shareholders' equity.

Some follow-up questions:

• Where is your balance sheet coming from in that it is out of balance?
• Are you importing your balance sheet from somewhere?  Is it in balance there, but not when importing?
• Not sure how you are out of balance unless you are trying to mix your book and tax balance sheets.
• Almost sounds as if your problem is that you need to have an M-1 to reflect income (unrealized gain on the books) on the books but not on the tax return.
• I agree with @Anonymous_ in that you may not be required to reflect a balance sheet on the tax return, however, I believe it is just a helpful item to have and maintain.  It does require understanding that there will most likely be book and tax reconciliation items as noted above.

I am having the same issue. The only tax document I get from Fidelity is the 1099 which basically just shows what dividends I received.  I didn't sell any stock however I have unrealized gains. I don't see wither on my 1099 or in TurboTax Business where M-1 line 7 which might be unrealized gains is detailed. I can surely calculate it myself, but it seems that should be a pretty common TurboTax situation that the software could walk you through a little better.

Thanks