Pokemon Emerald: Items are in the right bag using the app, but when I load it into a cartridge, they go in the wrong slots

[thataccordguy1]

So I goofed on an action replay and lost all of my HM's. When I use this to put them back, it removes a ton of items (Mystic Ticket, AuroraTicket, Old Sea Map and others) and then all the items it does keep, show up in the wrong pouch when the game is played. Can anyone help with this? Attatched is a copy of the game file I am trying to save. 

Pokemon - Emerald Version (USA, Europe).sav

[AlamosIT]

Somehow you have corrupted that part of the file associated with correctly recognizing the save file, PKHeX thought that it was a Ruby/Sapphire save.

I fixed this, but there is still something wrong with this file. At least now it reads correctly as an Emerald save file.

Pokemon - Emerald Version (USA, Europe).sav

Edited March 1 by AlamosIT