This issue was never resolved, and filing on paper is not a valid solution, so I had to make several overrides to make the return calculate properly.  Next tax season, I will need to check to see if the changes I made transferred or if I will need to adjust the returns again. 

In this day and age of technology, clients do not want to hear that my software provider is unable to fix a calculation problem/efiling issue.  I certainly hope, during this non busy time, a solution and update is forthcoming.