It's important to understand that, if you qualify for an exclusion of your active duty military pay, you may have other income that subjects you to West Virginia's state income tax, accounting for the tax due. The fact that you owed state tax last year would seem to indicate this possibility.
Along the same line, it's worth noting that West Virginia also includes some items in income that your federal return excludes (see Modifications Increasing Federal Adjusted Gross Income on page 4 of Form IT-140), which would result in a WV tax on items that wouldn't be taxed on your federal returns.
And finally, you might also notice that line 34 of Form IT-140 refers to an exclusion of Certain Active Duty Military pay, and refers to taxpayer to page 18 of the form instructions. Apparently not all active duty pay would necessarily be excluded.
Without knowing your overall situation, it's difficult to tell what might be causing what you're seeing. Please provide further clarification if you think it might be helpful.
(The items referenced above can be found in the Forms and Instructions Booklet available at West Virginia's Individuals income tax page.)
