(IANAL, but my business law professor was...) Contract law says that if you say you'll take X paid "shortly" instead of the full amount Y in a situation like the OP describes, it does not prohibit you from collecting the remaining amount later. Even if you sign a contract that agrees to settle the debt, that contract isn't valid because the employer is not providing any consideration in that instance.

Having said that, I was in a similar situation and basically just gave up ever seeing the money for the same reasons others have already given.