Sorry, I WAS assuming it was RabidVWM. It could be something else, however, I'm not using software or modules now that I wasn't using on my old computer, except for RabidVWM. And correct, I could just be (and have been a few times) just typing something in to a word document, or into a web page, and all of a sudden the program loses focus. Focus could be given to a different program, or to the "desktop", I'm not sure, since the original window stays on top.
Also, this could be related to the problem that RabidCow already knows about, where you open the popup, and it will dissapear from focus being assigned to something else.