Taking TT out of the picture for the moment, are you saying your broker reported a 1099-INT Line 8 which is higher than the cusip-level interest breakdown they provided, by this "tax-exempt non-qualified interest" amount. I've not seen this term in muni interest reporting (a muni MM fund may have non-qualified dividends), do you have any breakdown or example what they are referring to?
If TT is having some issue with import etc just delete and add manually, though it sounds like you are entering manually and separate PA tax exempt from PA taxable - if so this is best way to do it, to get the correct accrued interest adjustments (TT doesn't know how to apply adjustments between Box 1/3/8 or PA/non-PA)