Why is the S-Corp balance sheet out of balance?

Walk away and look at it with fresh eyes tomorrow...seriously.

Silly question but going to ask anyways - you did enter the Balance Sheet information because just entering income and expenses will not create the Balance Sheet.

Things I can think of to double check

 1)Shareholder distributions   2) contributions    3) interest income

Do you know the difference between expense and expenditure? Example:

If there is debt, the principle is the expenditure which reduces the running liability balance. Interest and any fees are an expense. I've seen people enter the entire payment as expense, and later try to adjust the loan balance when they get a 1098.

Also, an S Corp has payroll. We don't know how that is being managed, but that's a common place to find this type of error.

Lastly, you might try thinking of this differently: "After entering Taxpayer income and expenses for his S-Corp"

You are entering the S Corp's income and expense, as an operating entity independent from Humans who are the shareholders. Your tax filing is the S Corp. They are not "his" income or expenses.

Are you working from a trial balance?  One that shows all the assets/liabilities?

You entered "income/expenses"....  the difference between those impacts the cash balance.  The software doesn't do that math for you.