What type of cartridge are you using? I tested with EZ Flash, and was able to load my save on GB when using the "backup save" prompt when the cartridge boots. On emulator I had no trouble; it would create the .sav file which would allow me to load properly any time I booted the ROM.
I'm not doubting there could still be an issue, though. Give me more details, and I can look into it. I am also working with someone on the "official" physical release now, and making the sure the save is fully functional in that version is a top priority.