Something else to check on also...
Look at his Military W-2, and make sure that box 12 has a code Q with a $$ amount after it.
Some Possibilities as to why:
1) IF that code Q and $$ amount is not there on is official W-2 form, then that is why they IRS is questioning the combat $$ deferment.
2) IF the code Q and $$ is there, then there might be a data miscommunication between DFAS and the IRS about that value....OR
3) ...either that or the box 12 value you entered in the software (mistyped), when you entered that W-2 didn't match what was on his actual w-2
____________*Answers are correct to the best of my knowledge when posted, but should not be considered to be legal or official tax advice.*
