Assuming that you have the latest BIOS and drivers, I would also check bulletin boards for your specific system to see if others have noticed the issue you're reporting with other games/apps -- that is, "flicker" when running in 3D mode.
Also, note whether other games on your system exhibit the issue that you are seeing -- if it's only your game I suspect an issue in your game's coding, but not being familiar with what you are doing I can't make any specific suggestions. If it's all 3d games/apps then it's likely something with your configuration (drivers, BIOS, hardware, etc.) that's causing the issue.
So realize that when Intel GPA runs, it "attaches" a DLL to your process so that it can trap various calls that you are making. Intel GPA then inserts calls to the driver (and other system calls) in order to gather statistics and display them as an overlay on top of your game. So the system/driver calls that we make may indirectly impact the synchronization of your game with the device. Normally there is no noticeable difference in the game (other than a slight reduction in the FPS due to the small overhead), but obviously something else is happening here, which makes me suspect one of the issues mentioned earlier in this reply.
Hope this helps.