Virginia State Tax married filing seperate

I am in the military and my home of record is Texas but have lived in Virginia for 2 years with my spouse. She had a job in the state of Virginia for most of the year. We completed our federal taxes and files jointly with no issues and have already received our return. When trying to complete the state taxes it transferred our information and all of a sudden says we must file "married filing separately". This has never happened, so I am confused about how to rectify the situation.