In my case, the only game that is not workng is New_Super_Mario_Bros_2_USA but this has been like this since 1.2, I don't know why. The european version of the rom does work for some reason...
Some reports indicate that the dumped saves are incompatible, even if it was created on emuNAND.
New_Super_Mario_Bros_2_USA loaded fine for me, super trimmed.