There are a couple of boxes to the right of the sig in the prescription writer box. When I say the prescription box, I am not talking about the administrator options or prescription options, I am talking about the box that appears when you click on the prescribe button in a note. It has options such as omit signature, include DEA number, etc. You probably have the 'omit signature' box checked. You need to un-check it. If this is not the case, then re-upload the signature in the admin section under users, exit amazing charts, and restart computer (this is what tech support told us before we realized we had checked the omit signature box by accident).
Edit: If you are seeing the signatures on the letter writer, you most likely have the 'omit signature' box checked and have no problems with the actual signature files you uploaded.