General :: Diagnosing Heavy Cpu System Usage?

I have been encountering lots of heavy system cpu usage. It is sporadic, last for about 10 minutes, and brings everything else to crawl (latency of even typing characters into an editor or a terminal is painfully slow). My computer is an i7 quad, and all 8 logical cores fire at near 100% during these periods. I can see the usage clearly with htop. The red bars in htop indicate system use (I have attached a screen shot for an example). However, as there is no process per se, I have no clue what is causing it.

It is something I have to fix as the computer becomes unusable periodically throughout the day.I One thing to add, I am using the computer as a ltsp server on ubuntu, attaching to it using two thin clients. There is always heavy ethernet traffic through the second ethernet card. I don't know if this is related. However, I do think all this problem began when I installed the ltsp and switched to using a thin client.