@chnapy I noticed something while using the program. In the screenshot, I have PKHEX and your program open and showing Box 1. If a pokemon is in the party, and if the same type of pokemon is in a box, then that pokemon does not show up in PKvault. You can see it from the blank spaces for venasaur, charizard, blastoise, and raticate. A version of each is in my party.
You have a great program, please don't think I'm being negative. Just giving early user feedback.