Check to make sure your anti virus, disk defragmenter and anything else you might have that can be set to do a background scan is not active. They may be mistaking game play as system idle time and are running their tasks while you are trying to play.
Other possible culprits are P2P software, FTP softwrae etc.
Punkbuster will occasionally interfere with game play while it scans your system for cheat files and patches. This is annoying, but normal. Try playing on a server where punkbuster is not required and turning it off if the game allows that. If it is punkbuster you may be able to reduce interference by adding more RAM, defragging your HD or with a dual core CPU. Any of these upgrades will reduce the impact of background tasks like punkbuster.
Also if you HD is set to allow it to spin down when unused try setting it to always on in energy savings.