I used to see that happen on my Droid 1 when it was off for a while. It didn't run slow, but the idle CPU was 0%. When I dug into it, the front page shows the system CPU % was pretty high(instead of user). I chalked it up to the phone accounting for the wakeup resources.
You mention the phone is slow. On the CPU tab, is there anything at the top when this happens?
Robert