To quote on the SNES9x PS3 changes: Build 4.4.3 (11-01-2010)
Autodetection of Super Scope/Mouse/Multitap had a bug in it - after you loaded a Super Scope/mouse game and then tried to load a multitap-compatible game, the game would attempt to hook up the Mouse/Scope instead due to an error in a switch/case statement. Fixed this.
Autodetection now works as expected. Please upgrade to 4.4.3 as soon as possible to avoid inconvenient problems.