I had the help window docked with the mode set to "related topics", if I close the help window the slowness goes away. In Flex Builder 3, I always had the help window open and set to "related topics" without any noticable performance problems.
Try turning off LiveDocs (it's in the top of the Flash Builder preferences page). We've found a bug in Java with http requests not timing out when they should. It's fixed in JRE 1.6 so this only repros with JRE 1.5.
Hope that helps!