You are correct. A resident of PA who is active duty military stationed outside of PA on military orders does not pay PA taxes on military income. You should exclude your active duty pay from PA income.
First, be sure you have indicated in the "Personal info" section that you are military and PA is your resident state.
Next, when you enter your Form W2 for your active duty pay, be sure on the follow on page entitled "Uncommon Situations" you have selected "Active Duty Military".
Finally, in the PA state interview you will arrive a page entitled "Compensation Summary". There you will find your active duty Form W2. You will need to "Edit" that form and select that it is non-taxable to PA.
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