So, after further testing with the Live CD and the regular install, I was unable to get the problem to happen a second time with the live cd (it happened only once with the live CD). I was able to regularly experience it on the regular fresh install. The only difference? the Nvidia graphics card driver! On the installed distribution I enabled it, on the live CD, you cannot. Once I disabled the nvidia graphics card driver (current version) the problem went away. I think what must have been happening was the image of the screen was freezing, but not neccesarily the USB ports..but I couldn't see that since the screen was frozen. I do now have a new set of problems though where if the nvidia card is disabled the system has problems switching between and logging in and out of multiple user accounts (the screen will just go black and nothing will happen).
So should I be changing the bug to the nvidia package? Should I be filing a new bug about the black screen of death when either switching between user accounts or trying to log off one and go to the other?