Active duty pay is not taxable by PA if it was earned outside of PA. If that is the case, to get a refund you would need to amend your PA returns. Note that this only applies to your active duty pay, all other income (interest, dividends, cap gains, etc) is taxable to PA as your home of record.
See: http://www.revenue.pa.gov/FormsandPublications/FormsforIndividuals/PIT/Documents/rev-612.pdf
Include a copy of your orders assigning you outside of PA.
