Performance problem from periodic high CPU usage, please help

[shortles]

I've just started having a problem where my computer becomes periodically unusable for chunks of time, like 30-60 minutes.
Everything is going along well and then it slows down to a crawl.
In the task manager, under performance, I see a crazy amount of activity, sometimes pegged at 100%, sometimes less. But even when it shows the cores around 50-70%, I can't even right an email without significant lag.

It's a Dell, Windows 7 x64. i7 processor, 16gb of RAM.
The thing is, when I look at the applications running, none of them account for all the activity.
When I look at processes that doesn't add up to all the activity I'm experiencing either.
I got something called Process Explorer which gives a more thorough list but that doesn't show very high activity either for any process.

I ran several virus scans while the computer was booted into safe mode with networking. One of them caught some stuff, but subsequent searches came up clean.

I ran a tool to clean up the registry.

I can't figure out what is causing the problem and I don't know what to try now. It's weird because after a while the activity will just stop and I can use my computer again. And then just as mysteriously the problem will start up again.
Thanks for any help.

 

[Pancakes]

Sounds like you got background programs running try control alt delete check and checking task manager to see what processes are sucking up CPU and you could try config.sys check your startup services are running.

 

[shortles]

Thanks for the response, though the problem I'm having us that the processes don't account for all of the activity, I checked both the task manager and used process explorer which is more thorough.

 

[Pancakes]

Did you check start up services

 

[shortles]

Yes, and shouldn't those show up in the list of processes anyway?

 

[Pancakes]

Do you have a schedueled tasks running like defrag

 

[shortles]

No, the only thing I had was Microsoft security essentials and I turned off scanning for that to see if it made a difference.

 

[Pancakes]

You should try downloading other antivirus programs and run it in safe mode maybe

 

[divaker]

Install malwarebytes and eset nod32 and scan with both. And enjoy idle pc