I had already thought of that. I pressed C. Exited the game, went back in, pressed C. I still have the shuffle and no ability to run. I guess I'll just go back to my first game save and go from there.
I'll look into it as it might be a conflict with the crouched/not crouched "if" script. The game might think you are standing when you are crouched and it just bugged out. I never ran into that before but I will look it over. If you can reproduce it consistently please let me know how.