The save files for VBA are vary. I don't have such kind of problem,i guess. Here is how i can easily transfer the save files between VBA and gpSPhone in my iPhone.
First,I change the various save file type into ".sav". You will notice that the VBA save with ".sav", ".sa1", ".sa2", etc. but gpSPhone only provide the save file type of ".sav". Oh, by the way, you can't transfer ".SGM" files to play in gpSPhone. When you change the file type and tap "Enter" key, the windows will ask you a question saying, "If you change a file name extension, the file might become unusable. Are you sure you want to change it?". Choose "Yes". Then, the file name is changed. I recommended you to have an another copied file of the save file you are changing in some place safe for the backup so that if something wrong happen, you won't lose your original save file.
And then,I open the "PC suite for iPhone" application to transfer the files from the PC to iPhone.I'm sorry that I don't know which application to use the file transfer for ipod touch and i don't use iTunes for file transfer so i can't help much about this.
I transfer the save file to the same directory where the rom files ".gba" existed. Normally, they are under >var/ mobile/ Media/ ROMs/ GBA . There shouldn't be any folder like "battery" or something. The most important thing is you need to have exactly the same file name of the save file with that of the rom file you have there. E.g., If your rom file under that path is "Metroid - Zero Mission.gba", your save file must be "Metroid - Zero Mission.sav". You can't play if you have the file name as "Metroid-Zero Mission.sav". Even the space count. I think this is where you are wrong at but I'm not so sure.
Oh, if you can't transfer directly to that directory from PC to ipod, you can change that with iFile or something in your ipod. You can get iFile freely from Cydia.
If you want to transfer the gpSPhone save file to VBA again, you just have to go from bottom to up. You change the file type only when it's in your PC. Remember, always always have a backup file. You will regret it when you lose the save file you are working with.
Sometimes, I don't know why you can't play with the VBA save file, even in VBA. When I played "pokemon-firered" in VBA, I couldn't save the game. But, when i play in the gpSPhone, it's ok. So,I got an idea. Next time, when i play a new game, I will start with gpSPhone and only after that, I will play with the save file from the gpSPhone in VBA. May be I missed something in here but I'm ok with this idea.
Hope this is what you need.
