Turbotax has a problem calculating the Net Income (loss) Per Books -- I haven't the foggiest idea how it arrives at the number it arrives at. I recommend overriding this value, which is found in Line 1 of the form "Reconciliation" -- calculate the Net Income (loss) Per Books yourself.
1. The simplest version of Net income per Books (same thing as "Net Income") is:
Net Income per Books = Revenues - Expenses
Revenues is your total income, and expenses are the business expenses that you are deducting.
Basically, Net Income = Taxable Income on line 28 on Page 1 of Form 1120.
2. If you have Schedule D with capital gains:
Net Income = Revenues - Expenses + Capital Gains
3. If you also have Expenses that were not deducted then:
Net Income = Revenues - Expenses + Capital Gains - Non-deducted Expenses.
