If you can't figure out where that number is I would back up the return. Then I would delete the entire W-2 and start again. Enter everything exactly as it appears on the W-2. If there is a state pickup it will show in box 14. But before I would enter that W-2 I would go to the MD return and see if that subtraction is still there. If it isn't then you know there was something quirky with the W-2. If it is gone, then it was the input of the W-2. 

Don't check any boxes unless they are checked on the W-2.