Possible background service such as Microsoft updates.
If Vista,this could be the service Superfetch.
To stop this service;
Start and type SERVICES and return
Scroll through to Superfetch and disable this service and reboot.
If xp,turn off auto updating from Control panel,automatic updates/reboot.If things settle down we know its the MS updates causing the problem.
Also consider your startup programs;
start / run and type MSCONFIG and return.
Select startup and remove all the ticks but leave your firewall and antivirus ticked and reboot.If a laptop,leave the synaptics listings alone (do not untick them).
Same for Vista except type in the start box MSCONFIG and enter,agree to any UAC prompts.