I don't work with U-paint, so I can't help you there. Hopefully, some who does will come here.
In the meantime, try creating your files and then seeing if you can open those. If not, then there may be a problem with U-paint in general, but if you can open those files, then it may be a version conflict though I don't see why they would put incompatable files on the same-disk as the program. You never know, though.
I didn't make it!
you can only open the .upp files out of your upaint\characters map