There is some sort of problem with Minish Cap saves in VBA. I own an EZFA cart which is compatible with the .sav files used by VBA. If I backup my save to my harddrive and attempt to run it in VBA, all save data is erased. The 64 KB file also drops down to 8 KB, so that's something you may want to check for, alucard_br.
On the other hand, if I backup the save and never touch it with VBA, I'm still able to restore it to my cart just fine. It's only when VBA is involved that the save data is erased.
I think Mario Pinball Land works the same way, though I haven't run tests to confirm it's the same exact thing.