Yes, all of it is accounted for. Ok, so they are doing things correctly on their end, it is just an odd situation that is resulting in me owing at the end of the year. Yes, I currently am filing as Single, 0 Dependents, with an additional $50 per paycheck in federal taxes. (this is only done on 1 pay check if I receive more than one in a pay period)
I guess I will just add an additional $50 to my state withholdings so I don't have to deal with a big lump sum at tax time.
Thank you @DawnC for all of your help.
