There's no known issue with this deduction. If you've entered your information correctly, your active-duty income will be excluded on line 15 of Form PIT-1
You initially deduct active-duty military pay on line 17 of Form PIT-ADJ. Your total deductions and exemptions from that form are then claimed on line 15 of Form PIT-1.
After accounting for medical care expense deductions on line 16 of Form PIT-1, New Mexico taxable income is computed on line 17. The New Mexico tax on the line 17 amount is then entered on line 18.
If this doesn't address your issue, feel free to post back.
See LINE 17, Active duty pay for United States armed forces in the Instructions for Form PIT-ADJ for information about the deduction.