To clarify, I think I am having the same issue. I have a mortgage and a HELOC which together have a balance over $1M and which were issued during the period before the limit was reduced to 750K. It does not appear that the software is calculating this right.I can go into the mortgage deduction form and see that it is not filling in the worksheet with the average mortgage balances and it treats all my mortgage interest as nondeductible which of course results in a large tax bill. I have overrides the value on Schedule A with the right amount (calculated by hand) but I imagine I won't be able to file with this done. Is this essentially the same issue being reported here?
