I've had this problem for ever. It is especially noticable and infuriating when I try playing games in windowed mode but also when I am working on GPU-heavy programs like Photoshop or AutoCAD:
When I have more than one window open at the same time and they are overlaying my Windows 7 will sometimes switch to the one in the background when I click on the top one. Sometimes it will keep switching between the initial one and the one underneath very quickly (a few times per second) until I alt-tab or click a few times on one of them. When I try playing games in windowed mode or borderless every click anywhere on the screen will cause the game to turn black for parts of the second, show "not responding" and then continue running, even if there are no other windows open at the time but the desktop. This has never happened when playing in fullscreen, however.
My laptop specs:
Accer Aspire 5736Z
Pentium® Dual-Core CPU 2.30Ghz
Mobile Intel® 4 Series Express Chipset Family (I assume that's my graphics card)
4Gb of RAM
Running 64bit Windows 7