To save, you need to set the save game to Options --> Emulator --> Save Type --> Automatic --> Flash 128k. Deleting your vba.ini and re-setting the controls works for some, but not all people.
If that don't work, you got no choice but to apply the patch and restart from scratch,
there is no other way that i'm aware of.
You may want to backup your .ini file before you delete it,
without it your save may be screwed.