Similar problem: Mortgage paid off during year, deductible interest below threshhold amount so Form 1098 was not issued by lender. TurboTax Desktop edition would not accept $$ values for Beginning Principal, Principal Paid, Deductible Interest, etc. Completed rest of return to point of E-Filing but software would not e-file unless Principal values were posted. Finally resolved problem by opening the Mortgage Interest Worksheet and overriding each field (right clicking for popup menu or CTRL+D) and manually posting amounts.
