I have posted this before as I have a similar situation.  This is not a ProSeries specific problem it's the state tax returns themselves problem.  Apportionment at the business level is typically a calculation of sales, property and payroll within that state.  But receiving a K-1 for a business from a business is not something the state tax returns are designed for.

I have a business client with 23 states.  I called all 23 state tax agencies.  Only  for Alabama did the agent walk-me through how to "get around" the software to report the apportioned income.  Bottom line, in all 23 states I had to force the state return, knowing the presentation was incorrect, but the bottom line was correct.

I also tested Lacerte (as a demo).  It did a better job than ProSeries but it wasn't perfect either.  

These 23 state returns took me a few days to complete.  In my cover letter to the client I explained the presentation versus bottom line issue so if any state sent notices, I was on record.

I told the client I was handing this return off to a large firm.  After a few months the client called me and said he wants me to handle the return as the large firm would not call him back, would not respond to emails.  Bottom line, their service was lousy.  So even though I wanted to get rid of this client, I cannot.