Hello Kirk,
I can reproduce the following problem:
I try to upload a JPEG, saved from CANON .CR2 (RAW). If the file upload stalls (in the case of a broken line) I klick <ok> in the warning window. If the line is ok I mark the file in the UPLOAD-POPUP window and try to resend the file (<resend queue> button). Now the fileextension changes from .JPG to .CR2 and now PM sends the RAW.