You should be able to select the controller by clicking the arrows before pressing accept with the mouse.
The controls screen can also be accessed in the title screen by pressing up.
That fixed it! thank you so much. I'm glad i found that bug too
Also when you pause during the cut-scene of Robotnik taking the emeralds after the first zone, the game freezes completely. I didn't know if you knew that. Figured that you should
Did you use Enter to exit from the pause? In any case it will be solved when 1.07 will hit!
