Never had this issue anywhere else. I, typically, disable my mouse pad and run a USB mouse, but just to be safe I ran through it with my mouse pad disabled and no mouse (using the space key to move dialogue along after the fight) same issue.
However:
I did get it to work, the weirdest thing worked, as soon as I finished the light puzzle I brought my mouse up to the top of the screen hoping to be able to save the game... The menu was disabled but opening the drop menu paused the game for a second, this seemed to reset something and after this point everything worked fine. I did the same thing as soon as I entered act II (I am not sure if this helped as well but I didn't want to take a chance, and if standing on one leg makes it work once, well... you know haha)