PKHex with cia saves

[Blaze Uchiha]

The new version of pkhex is giving me problems. I load my save in it and go to edit my wondercards. First my 20th aniversary celebi wondercard doesn't show up in the list. Next I add all of my downloaded wondercards in it and reactivate my previously used wondercards. Then I save my wondercard info and export my save back to my sd card. I go through the normal process of putting my save back into the game then I load my game. The wondercards I've added don't show up and the previous wondercards I've used are still used. Thinking I did something wrong I exported my save again and reopened pkhex.All of my edits were still there though. What is going on with this. Out of all my times using pkhex this has never happened to me before. Is this a problem for anyone else? Also it turns out that anything I edit does the exact same thing yet PKHex works perfectly with my cartridge version of Pokemon Ruby. So does PKHex only work with the physical copy of the game or can I use it with my backup copies?

[Kaphotics]

You need to set wondercards back into a slot; the 24 picturebox preview is where they are displayed.

Unused cards are not faded out.

[Blaze Uchiha]

You need to set wondercards back into a slot; the 24 picturebox preview is where they are displayed.

Unused cards are not faded out.

Yeah I've done all of that. The game itself is the exact same save as it was before I exported it. I've tried several times to edit the save and made sure I've saved it several times before exporting it back to my SD card. It's not just wondercards though it's every edit I make. Like I said this works perfectly fine on my cartridge version but not my cia backup.