Get a screen shot of your processes when all is well.
Then the next time it acts up, take another screen shot of all your processes, and compare.
If its nothing of the above, there must be something grabbing too much attention on the CPU or something, during your times of complaint.
Another thing to try for a spell, is to change your "open program" to use a sound bite.
I used the hallo deck door from Star trek once. to catch an offender.
Or any of the ones already provided with windows, like tada.wav
So if you hear it, while in game and you know dam well you didn't start something, you can jump out and look at processes and try and catch the offender.