No idea about joysticks. That should be placed on a different thread here at Qhimm's. Someone else may know.
If you are using Steam version of the game, then you don't need Aali's driver. If you aren't, then you do. I keep forgetting that Steam doesn't need it.
If you are using Steam, please make sure that you are using fresh original files (then delete Backup-Reunion folder, which is in the game's root folder). Reinstall The Reunion. If the problem persists, try to uncheck the 60fps mod, as that *could* cause an issue with battle.