To the person having trouble transferring the save file, there are a few things you should check.
I don't use no$gba or whatever but I have used VBA and there are several options when saving a game. You can do in game saves or save your state.
If you save a state every emulator treats this a little differently(I assume) so it may be impossible for you to transfer it.
If you did ingame saves you still might be out of luck, because the GBAOID I am pretty sure only works with 128 kb flash save types, now when I was using pokemon firered on VBA the rom default saved to 64kb flash. However I started a new game with 128kb checked and did in game saves and was able to transfer it to the gbaoid flawlessly. Also people who can't figure out how to work it take some time and read the instructions it is quite straight forward and the guy behind it has offered an phenomenal amount of support and updates for this application. His newest update even included a speed up function for RPG's to make those long periods of leveling up more stomachable.