When I said that my system is updated, I meant all of the software, plugins, etc. that are on my system. Adobe Flash is at version 10.1 I believe. As for it being a web site or the browser that I am using, I figured it wasn't the cause because this is happening with no browser open. It happens when there are no apps running at all. I restart my computer and the problem still persists.
It generally happens whenever I try to do something (open a program, close a program, change system settings, etc.). It also seems to happen randomly. Like right now, it isn't doing it, but earlier today it did it for about 4 hours, then stopped and started running smoothly.
I have tried repairing disk permissions, running virus scans, etc. and nothing has helped.
Actually, as I started typing this message the problem has started again. Every so often while I type the spinning beach ball of death will pop up and nothing will work in the browser, then it will start working again.