Okay... yeah this sounds like something is running in the background. Like an updater or a scanner or something. Have you disabled startup programs? Anti viruses? Pretty much anything that works in the background?
I mentioned the Sweetwater Optimization guide...
http://www.sweetwater.com/sweetcare/articles/pc-optimization-guide-for-windows-7/ As I said ther are certain things in there that don't play well with Sonar but I forget which. However this was what was recommended to me by Cake tech support. Mainly look at the parts about disable programs and letting things like your drives and ports go to sleep (power management).
Also you should probably do a virus/malware scan to make sure nothing hinkey has creeped onto your system and is trying to phone home. I use avast for more thorough scans then Malwarebytes and sometimes Spybot Search and Destroy then use CCleaner to clean up the registry and whatnot.
CREATE A SYSTEM RESTORE BEFORE ALL THAT... especially the CCleaner stuff (but it CCleaner will prompt you to create a restore point anyway). If some goes wrong then you can return to that point.
There is the DPC latency checker too which I've never used but supposedly it can hunt down weird crap that causes problems like you are describing. Really though you should just call support to get this worked out if you can.
Good luck.