We've been continuing to have this problem on some computers.
Some of the discussion above was focused on our nightly scan that doesn't complete in the 3 hour window given it, so it suspends until the next day. This is not the issue.
The issue is the arrival of new definition files.
When a new definition file arrives, the "Scan Log" in SEP shows "Scan Complete" and it takes about 1.5 minutes on my computer.
However, for the next 30 minutes or so, the entire computer is sluggish. Typing in any program may freeze up for 10 seconds, then be okay for 10 seconds, then freeze for another 5-10 seconds, etc. During this time, the Task Manager shows very little activity. However, "System" task appears to be accessing 'random' files all over the computer.
I've set my client to not use a proxy and tried turning off various feature (Insight, Download Insight, etc) but have not found a cure for this problem. I had the full logging on for a while, but after collecting 3gb of logs and not finding anything interesting, I turned them off again. However, that was when looking for the issue with the nightly scans. I've turned the logging on again, and will review it after the next "slow down".
Any other ideas to explore?