The problem comes from the show desktop button which is a confirmed Guake bug. I never use the show desktop button from the sidebar, but realized later on that accidentally selecting show desktop while alt-tabbing is very easy to do (more so if you're unaccustomed to the alt-tab behavior brought about in 12.04).
I found a temporary fix as outlined by Stibbons by using "Hide on lose focus" in preferences. Keep in mind this will only prevent the alt-tabbing show desktop bug, and isn't ideal if you require a static terminal on a separate monitor. (I've disabled the sidebar button in settings > appearance > behavior - just in case!)
Stibbons said 19 days ago "I'll try to fix it asap," and as I was losing current tabs every few hours this temporary fix is HUGE timesaver.