If the CPU is not running at 99% all the time, then when the lag starts, look at the harddrive activity light on the front of your computer. Is it on while the lag happens? if so it is an access problem with your drive.
If not, then there is a program running in the background that is takeing up the CPU usage. considering you most likely have Windows for an OS, I would not be surprised. Do a intense check for viruses, and spyware/adware. Then try to start the game, and then go into the task manager under processes and try to find the program that is useing the CPU up. If the process is called SVHOST, then you pretty much hosed. SVHOST is a kind of roll up process that compbines a bunch of small processes into one. I have heard that there is a way to find out what processes are running in the SVHOST, but I have been unable to find out how.
Anyway, if it is the SVHOST, which there can be several. You can try to end that process. If you can't, your best bet is to reinstall your system. If it is another process, write it down, end it, and do a search on your drive and the internet for what the process does. You way be able to disable the process compleatly.
Good luck