I removed my amd64 installation of Gentoo and replaced it with the x86 installation so I wouldn't have to face the Flash issues anymore. I was also experiencing problems with Firefox, with windows mysteriously opening and making navigation difficult. I'm having the problem on the x86 side as well and suspect that one of the add-ons I installed is causing the problem. I'm guessing it may be the NoScript add-on. I'm working with very few add-ons right now and will add more, one at a time, making sure one of these isn't causing the issue, and probably avoiding NoScript unless I find something that suggests something else is the problem.
I'm also waiting to see if I will have issues with X crashing when using Mplayer, but am waiting for a moment when I have nothing critical running.