Hi,

I had RetroPie running on Mint for a short time and I didn't need to mess with the fullscreen options. All I did was add a startup delay of 3 seconds to the RetroPie entry. This stopped the issue. I would leave it as fullscreen and try that? I think this happens because if ES starts before X is running it doesn't launch. Not sure though but a slight delay should resolve.

Yeah I should have mentioned that as well. Controller syncs fine with my Pi3 running Retropie.

I finally got this to work. The key was installing both xboxdrvr and xpad. I also copied the working xbox 360 controller config from the wiki (here) and restarted the computer. After that, all the controls started working except for the d-pad. I had to go into the retroarch RGUI menu (the keyboard was also working now, so I had to use it to navigate the menu since the d-pad wasn't working) and adjust the controls for the d-pad in all the emulators. For some reason, it was the only part that wasn't working. I did notice that my triggers are handled differently for the two types of controllers. The 360 controller the triggers act as axis while the rock candy one is treated as buttons. This changed the axis that are used for the d-pad (which might also be weird. I would have expected the d-pad to be buttons, but that's no the case).

At any rate , I finally got this working. Hope this helps if someone else is having similar issues.