Here is how I fixed the problem that occurs in a LOSS scenario:
1) click on forms (upper right menu bar)
2) scroll down the left menu under "Form 1120S: S Corps" to "Sch M-1 Wks"
3) For each non-deductible expense item: remove the negative sign in the "Per Books" column
4) Click "Step-by-Step" in the upper right menu bar to return to the previous mode.
Disclaimer: I'm not a tax expert.
