This is a silly mistake that I just figured out as I was posting. Spent 15 minutes trying to figure out what was going on, so I'll post here in case it's helpful to someone else at some point:

Working on a return for an estate and checked the box that it is the final return. There was a with a large capital loss. ProSeries was distributing the final year deductions, but not the capital loss. Could not figure out why.

It's because the capital loss will not go on line 3 or 4 of the K-1, it will go on line 11 with the rest of the final year deductions.