Interesting problem
I recently discovered that multitouch wasn't functioning on my '08 mbp w/ sl. The 2 finger scroll worked, but not zooming or rotating.
As mentioned in an earlier post, I tried the fsck to no avail.
Also, I created a new user, logged in as that user, and found that all of my multitouch functionality was restored. I logged out and then logged in as my normal user account, and again, functionality was restored.
Following a reboot, multitouch was gone. As an experiment I deleted the new user account. I found that after a fresh boot, multitouch would not work. However, after logging out, and then logging back in, multitouch is restored.
I have not tried turning off automatic logon to see if that is the issue, but I will try it next.
Update: Automatic login does not appear to affect the results.