how are you playing this game? thru a web browser, a game boy emulator program or on a real gameboy hardware? I am not experiencing that problem you are having
yea well what operating system are you using since you did not mention that in the first place, which is also equally unhelpful
also try running VisualBoyAdvance-M from another computer or a different OS platform such as Windows or MacOS
I run the VBA-M app from a folder or path with a "short" name that doesn't contain spaces in between (never using folders with really long names or paths), on SEVERAL Windows based computers and they all work correctly, including game saving & loading.