Sorry, this is not a definitive solution. Just something you can try.
Create another user on your computer, with same privileged level. But do not install or use Skype on that user. Reboot your PC and log into the new user. Try your favorite game. You may have to import some settings from the original user, or just start with new settings for the game just to see what happens.
Now then, use then fast user switch thing to just go over to you normal user. Bring up Skype, use it, then close. After that, switch back top the new user and start your game again. What happens? You might find the problem is attached to user settings. Skype modified user settings and failed to restore them.
Tell me I mad a bad guess.