Can you open Task Manager when this happens...or have it open ready...to see what process is using CPU time during this 30 seconds?
As it's a regular occurance that happens for 30 seconds or so you should be able to narrow it down if there is some background process causing excessive CPU usage.
Are you running System Restore there &/or indexing service actively?
Alec, what exactly does the indexing service do? I think I've turned it off anyway. Am I right in thinking it just speeds up searching the harddisk, by caching locations of files etc. or something like that?