I'm having the same problem in Turbotax Deluxe. I live in NJ but sometimes work in NY. My wife is a NJ teacher. Last year we had to file NY manually because of this issue and it a little disappointing it hasn't been fixed. Following the suggestion of selecting NY "tax-exempt" still requires manual filing. It seems there need to be another choice "Not related to NY" or "Non-Resident & Non-NY Pension" that would allow NY to be electronically filed.
