I don't know about different versions saving battery in different formats ...
but I know that:
1) different *ROMs* have different *correct* battery format
2) vba-over.ini should specify the correct one for most known ROMs
3) different versions of VBA *might* autodetect differently (that only applies if the ROM wasn't found in vba-over)

As far as I can tell, battery saved with the wrong format should be "broken" no matter which version of VBA you use (or whether you use vba-over when loading).

IOW, I can't help you with this =)