It will all work out in the wash at tax filing time. But 50% withholding? First, you need to see what you have on the W-4 you filed with the employer. They are required to use what you claim on the W-4 you provided them, in figuring your withholding. Next, I would ask them to cite what specific IRS regulation they are referring to. If this is the benefits department telling you this, then it's not the fact that I would not expect them to have the first clue about taxes, but more the fact that "apparently" they think you're so stupid that you'll believe whatever they tell you.
