Per Lacerte, this is a program limitation.  To my knowledge, in 45 years of doing income taxes, IA has never sent any type of notice reflecting the issue.  At the moment, the simplest solution to come up with the "correct" answer is manually calculating the correct %, then increasing or reducing one of the items on the split return.  If IA ever sends a tax notice, I'm sure they would accept the "program" limitation issue answer once they realize the correct deduction was taken.