Windows remain behind other windows despite being clicked

This has been driving me nuts. Windows and applications I click on very rarely come to the front when I select them. It doesn't matter if I click on them directly or through the task bar. It doesn't matter if they're full screen or windowed. They'll almost always stay behind whatever window they're currently behind, and I have to slide everything around to get to the window I want. This is happening with all programs, from Chrome to Quickbooks. It's killing my ability to multitask.

I have two monitors. I run a few programs in the background, like Skype, Steam, Logitech mouse drivers, f.lux, synergy, as well as Start is Back and Stardock's Modern Mix.

I've already started troubleshooting programs, and will continue to do so, but in the interim, if anyone has any ideas or troubleshooting tips, I'd GREATLY appreciate it. Thanks.