Ok, I can't say that I've experienced a similar problem at any stage, but that won't stop us tracking this down!
The good news is that nobody else is experiencing this issue, and thus it's something we can sort out

-Grab a fresh build of the pitstop editor
-Make sure you're using the correct rom: The USA version only as the editor is written for the offsets included there
-Try loading the rom as a new project, and viewing the karts, select one and save it out, and then import it back in. This is the 360 test that's really proof of function. If there's no problems there then it's probably safe to say that everything working correctly. If you have another issue, go back and repeat the first two points to see if you can catch where something went wrong (grab a rom from a different site for instance).
I hope that helps!