My Google Fu has failed me and I can't find a solution that isn't a pain in the butt. I'm returning from a 3 year hiatus and can't figure out how to fix this. I have 3 monitors (but we can assume it is dual monitor if that makes anyone feel better). When I'm windowed, the mouse can leave the EQ window. Great. I expect that. I hit Alt-Enter. Yay, now I'm playing 2560x1440 on my 27" monitor. If I move my mouse too far it leaves the full-screen app and an accidental left or right click (which happens a lot since I right-click to strafe), EQ minimizes and now I have to go hunt for the EQ icon and hope I don't die in the meantime. The only solution has been (and this is EXTREMELY STUPID) is manually going in and turning off my other monitors. That is a huge pain in the ***.
My solution if I was in your shoes would be to download Display Fusion. Display Fusion makes more 2 + monitors a lot easier to run and includes a lot of neat settings that can help you out with EQ.