Hi, I recently started playing Platinum on an R4 and and only just started using Pokesav. I decided to try the program out with small things (editing my starters, getting fossils, unlocking all Poketch apps) and had no trouble.
I'd deposited 2 of my Pokemon into Box 1 to make room for the Fossil Pokemon then set about resurrecting the Shieldon and Aerodactyl. About halfway through, I realised the Skull Fossil I'd made didn't appear in my bag, but I didn't think too much of it. I could have just gotten another one. So I deposited the Shieldon into Box 1 and saved right in front of the computer. I'd quit the game, took the Card out of the R4 cart, connected it to my computer and added the Skull Fossil, along with some extra items. I saved a backup of the original file like I usually do and saved a new one onto it.
However, when I started playing Pokemon, the Fossil was not in the bag and when I'd checked my computer, all the Pokemon in Box 1 had vanished. I checked the save file i put onto my cart in Pokesav and my Pokemon are listed in the Box. I then put in the original back up, hoping to get them back, but the Pokemon still didn't appear in my Box.
So I guess the question is; why don't the pokemon I make in Pokesav inside the storage boxes appear in-game? (Sorry for long post, wanted to make sure I didn't miss a crucial detail)