So using the latest revision, revision e, when I generated a pokemon, and exported my save as normal, I re-opened it to double check, and nothing was there.
Any changes I make to the Party-Battle Box stick, but anything I put into the Box tab, doesn't seem to be saving.
Any modifications done to anything int he SAV tab, also stick just fine.
EDIT:
So after making this post, I decided to generate my pokemon then save them using FILE > Save PKM.
I then reopened the save, and drug the PKM files back into the Box tab, and exported my save again.
I reopened the save to see if it stuck, and that seems to have made the pokemon stick.
Hope this is helpful to the Devs, I can try to provide whatever I can to help address this issue.