Have you tried restarting the game?
If the problem persists please send us an email, we'll try to troubleshoot it with you. :)
Apologies, but I don't have your email so I'm putting this here. Hopefully at least doing so has the silver lining that if anyone else has this problem they'll get more information. Restarting the game helped, though so far my run-throughs of the game trigger the issue again and I have to restart if I want to use mouse controls. I've found that the tab and enter keys allow me to select options, and space and escape move the game forward and bring up the menu respectively. It's particularly odd that I can use the mouse to click through the main and in game menus, but not use them anywhere on the screen while in the midst of the game itself...