This is a save format problem, not a save folder one. You can switch between different save formats on the VBA menus like this:
Options -> Emulator -> Save Type
Then play with the different options. Change the save type before you load the game, if doesn't work, quit the emu and try again. I think "Flash" & "Flash 64" might work, as it look the save type it uses its " FLASH512_V130 (512Kbit)". I think you got the (E) version btw.
If still don't succeed, the save sates options will do the job, just use menu:
"File" -> "Save Game"
then check
"File" -> "Load Game" -> "Enable auto load most recent".
Now whenever you want, save you state, then you might quit and load the game later; your progress will be auto loaded. Hope it helps
Also play it and load in other emu as Rascalboy Advance or BoycottAdvance, as are more save files compatible, then copy the save file to VBA sav folder, it worked for me some times