PJ64 uses a database to verify the Roms, so if an older version recognizes some game, an updated one might have this entry removed from its database because it might have been identitfied as corrupt/bad dumped, etc Rom. PJ64 Usually labels these Roms as it should (bad dump, etc), but sometimes mark them as unknown. You can load them anyway from the "File" -> "Load" menu.
Also you might try to update the database (.rdb file), take a look at the PJ64 official forum


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