one other thing i noticed while trying to figure out the issue is that it seems that PokeGen doesnt keep within it's memory the data of a nickname, so say for instance i create a pokemon then i right click a slot in a box and click set, then go up to tools and hit reset controls to clear the board to make a new poke. if i right click the newly made pokemon to choose view data, all of the data is there except for what i had custom set for the nickname. i tried many different types of nicknames as well...
i dont know if this directly ties into the issue i'm having but since i recently noticed it i thought i'd give this info over to you