Some other things to check:
Are you running the Wacom tablet driver? It causes some random "pauses"
Is it centered around a certain time of the day? Especially the wee hours? BSDs run maintenance scripts to clean up log files and so forth. These are set up in /etc/daily /etc/weekly, etc... I've definitely seen these scripts bring BSD systems to their knees. It is also possible that some clean up scripts are scheduled for the first launch after install. If this is the case, that would explain the "four reboot" solution.
Also, check your Energy Preference Pane, perhaps the drive(s) is being spun down. I noticed this happening after every OSX install I did...
If it happens again, type "top" in the terminal or use Process Manager to see if anything is using inordinate amounts of processor time/memory.
-alex.