You've left out the most important piece of information: Did you negotiate the position as a 1099? If so, then why are you doing this to them? They held up t

You've left out the most important piece of information: Did you negotiate the position as a 1099? If so, then why are you doing this to them? They held up their end of the bargain, and seemingly more by "treating you as a full time employee". Trying to squeeze benefits out of them after the fact seems like a bad plan. Stick to the terms you agreed to. If not, then why did you stay more than one pay period? As soon as it was evident that they were not withholding taxes, this would have needed to come to a head before you worked even one more day for them. The fact that it didn't implies that it was in fact that other scenario and now you're just trying to wring extra money out of a company that you had agreed to contract for.