If you are using Gb64 03 beta, I think those errors mean dirty contacts with the transfer pak, so re-adjust the pak to see if you still get that error. Otherwise, try another controller or reformatting your sd card (back it up first of course), that worked for me (ive dumped basically my whole gb collection, saves, and multicart menus at this point).
If you are using edgb_loader (since you said GB uploader, was confused which you are referring to), you need to have a modded transfer pak to use the edgb with n64 games.