Umm, not really sure what to say because I've never had that problem when I tried to use the save option in the menu. I dont make hacks myself to realyl know but it might be that the rom you downloaded wasn't the right version or something. You could also try using a savestate in VBA by pressing like Shift + F1 to save and F1 to load.
i don't know why its happening to you but so far for me the game saves smoothly with no problems whatsoever. and yes you are right about the Flash 128k.. always check that first when playing a hack. And make sure that the ROM you patched is compatible with the one indicated in the hack. If it isn't then problems arise. You may need to post at the hack's thread about your problem. I'm sure they can help you further there
I have a problem with my games. When I got them in VBA and saved then came back to play it it was very glitchy and slow. The music was messed up too and it was going slowly when it worked fine on the first go. I also do not see the saved file on the game but the same problem happens. How do I get that to stop happening? I put it on Flash 128K. How do you save on them? I am using in game save. What should I be using? And do I need to unzip files? Do you do that by extracting them? Please help, I will be extremely greatful if you do. I am a beginner in this so please explain everything the best you can. Thank you.