First, I want you to uninstall the program. Make sure you manually delete the CFG folder when it's done. Also backup your MEMCARDS and BIOS folders if you like.
Re-install the free version. Then install the supporter version (if you have it). At this point you can put your BIOS and MEMCARDS folders back where they belong.
Get SimonMallion's 1.06 skin and copy the contents to /FpseCE/SKINS. Overwrite all existing files when it asks you.
OK, for Tekken 3, you'll probably be wanting to use the digital pad. On the main menu, you are able to change the pad type between digital, analog and GunCon. Make sure it is set to digital. The button is toward the left of the screen and the top controller is the digital one.
Now, go into the on-screen menu. You can tap on the icons that look like control pads to place them on the screen. If you want start, select, L1, etc. you can place them on the grid with relative ease.
You should be set.
If you are still having problems after this, remove everything from your phone that has anything to do with FpseCE, except the BIOS, games and memory cards. Install the program as usual, then install KowboyBebop's HD2 pack.
Platinum trophies: Uncharted, MW2, Uncharted 2, Resi 5, AC II, Fallout 3, Batman: AA, CoD: WaW, BlOps, FFXIII, BioShock, L.A. Noire, Deus Ex: HR, Uncharted 3, Heavy Rain, Batman: AC, inFAMOUS 2, The Walking Dead, Virtue's Last Reward, Borderlands