Sounds like you haven't applied the
Microsoft Dual-Core Hotfix. It's a patch for a flaw in the operating system that effects the way Pro Tools (and many
other programs as well) functions.
If you had actually read the link JMS gave you, and the subsequent link to the General Troubleshooting thread that is within, you would have come across this suggestion already. It's one of the reasons why he gave you the link in the first place.