If I was a betting person, I would say you are missing the check box which says "some investment in corporation not at-risk".   If I was a betting person.

I wish that was the case, but it's not. The "some investment is not at risk" box is checked. Thanks.

ProSeries treats Form 7203 as merely informational.  It does not 'do' anything.  You need to manually limit Basis by only entering the allowable amounts on the K-1 worksheet, then manually remember to carry the unallowed loss over to next year.

Are you saying that some losses are initially allowed due to some Basis, but then are restricted to non-allowed due to the At-Risk rules?

When I do the 1040 K1 and line 1 is a loss I click on supporting statement, and put in loss as on the K1, then an offsetting amount so the loss allowed (if any) is put on line one of the K1 then that amount is what is transferred to schedule E