If you can provide a save file and exact instructions on what you're doing that produces the problem, that's the only particularly useful information. This is, of course, if the problem is consistently happening.
Edit: Perhaps not. You're correct, there is an issue here, and I know exactly what it is. A recent change was made to prevent all Pokemon from being processed by PokeGen if they weren't edited. The way it's coded, it doesn't flag Pokemon that've been moved around. I also don't think I made it copy the flag that indicates that one has been edited, so editing, then moving, might not produce the expected result.
I apologize for not giving the report more thought initially. I'll probably release a new version soon to fix the annoying combo box selection bug and this, as they're both pretty significant toward usability.