All input errors should be fixed now...

So, moving it to the retropie allowed me to debug some errors other people were seeing on their systems- it turns out, I thought I'd removed a lot of beta debug code involving fonts and graphics before the original launch, but I'd left some in. And this was causing issues on some systems, and it would only effect the menus (which is why it was working fine in game, but only menus were causing the issue). I was able to remove that code, test it out on the retropie- and BAM. It worked. I tried it on several other low end Windows and Linux machines- BAM. Problem solved.

It wasn't the timer or the FPS cap as some people were erroneously suggesting, but rather something clogging the draw function and slowing it down due to the debug code. Should be working fine now, let me know if not.