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When I first read this post, I was away from home, so didn't due a thorough reading.

About Alt+F for FPS in RB3D. Doing so will kill about 10 FPS in your game, so when not using FPS in the game, your game will run about 10 FPS faster.

I use FRAPs to check my FPS, and every time I have used Alt+F while Fraps is running, my FPS in FRAPs takes a 10 FPS hit, however it is usually then showing the same FPS as the game.
Within the HASP and WFP RB3D folders, I deleted the old shortcut links, and created new ones, then created a new profile in the logitech profiler, and VOILA! They both worked. Unfortunately, I can't link the profile to the ReLoad option (making RotJ a no-go, apparently). However, then next thing to try is to load the game from the ReLoad shortcut (instead of booting it up from the Logitech profiler) to see if the game/joystick are still linked up.

So anyway, I now have three working versions (still haven't fiddled with RotJ--that takes some time), and all have acceptable to downright great FPS, and all work great with the joystick. I hope this helps others, and let me know if anything I wrote was unclear.
Glad to hear the game is running better now! For the joystick, have you tried Stanski's/Wailwulf's suggestion of simply making your joystick profile "persistent" so that no matter what game is running that profile is running? If that works for you, it should simplify your problem as the game would not be looking for any particular game to load your settings - the profile would just be already on.
Post edited January 07, 2012 by crazy_dave