I once had a loose cart connection to the SNES erase my Super Metroid save. Years later that same battery still works. I just make sure it has a solid connection. So it could be the adapter...
edit: ^ Dat Super Metroid save tragedy ;_;
Yup same thing happened to me. Several times before I just bought a new super metroid cart and used a different SNES just to be sure.
It's times like that where a password system is preferable to a save system.