Let me explain my set up. I have a windows 7 pc that I am trying to setup as a HTPC. I have a wireless xbox 360 controller that works great in retroarch. I have all my cores working great. I also want to control my pc with my controller when not using retroarch to watch dvds through it. I am using Xpadder for this. I don’t need a lot of functionality with my controller. I just want to map the mouse to an analog stick, and map return, escape, right click, and left click to controller buttons. I set that up and it works great. But now those buttons interfer with my retroarch setup. Is there a way to make retroarch ignore keystrokes from the keyboard that Xpadder is sending so that it just recognizes the game controller? I know Xpadder has autoprofiles, but I tried setting it up but it wouldn’t works. Any ideas?
Your setup sounds similiar to mine. I use Xpadder control absolutely everything. I don’t even bother with RA’s native controller mapping thing. (with the exception of analogue sticks, 'cause xpadder can’t do analogue 
)
Can you describe what sort of interaction is happening that you are trying to avoid?
Generally, though with exception, I will map PC functions to the 2nd page in Xpadder. That way I hold select to use them.
So like, I’d hold select and that turns the right-stick into the mouse and my LB/LT to left & right clicks, etc.