I noticed that too lately, sometimes it's taking a while to load the main page... always something. I'll keep an eye on it, in the meantime please let me know exactly the time when this is happening so I can check the logs for any signs of problems.
ie. Chat used to flake out always around midnight... I didn't clue in, but that's when I had crontabs set up to do automatic backup of database and archiving of the directories... I spread the processes b/w 2-4 so things should be much better around midnight.