The program is looking for taxable income when a Q is entered. If the 1099-Q is not income, it should not be entered. Tuck the 1099-Q into your tax folder. IRS Publication 970, Tax Benefits for Education states that nontaxable distributions should not be entered.
If your 1099-Q was not completely used for education expenses and room and board, then the taxable portion of the program is working. Please reply with the issue you are having for us to further help.