Iv been having the same issues as you when trying to get the gamepad to work properly. The way vorpx handles gamepad imputs doesnt alow for deep customization which is fine since there are programs like xpadder that fill that need. However the problem still persists because the internal gamepad seems to have inputs for buttons that simply cant be remapped and it seems to be causing problems with xpadder. When I start a game the gamepad works flawlessly but as soon as I hit the left thumbstick it brings up a weird vorpx menu with numbers that dont seem to serve any function and after I close that all my buttons are messed up. I cant run anymore, sheathing weapons makes me run forward indefinitely and the start and select buttons do other random things.
As a side note, these issues seem to only affect skyrim and farcry 3 as apposed to bioshock infinite, borderlands 2 and COD MW3 which work flawlessly.