The same problem hit me today...it was fine yesterday after I upgraded my FW. Though my shortcuts had stopped working, the Contacts and Dialpad touch buttons were working fine, as well as all three of the Hard Buttons.
Today, none of the home touch screen hotspots were working, as well as the Connect and Disconnect hard buttons.
Factory Reset didn't have any effect on the problem. I did notice, though, that the hard keys worked in applications, just not on the home screen, so I figured that a hard reset might work after all, since it's activated before the home screen comes up.
Ran a hard reset, which fixed the button problem but lost all my recent contacts (as expected). Since I'd backed up for the FW upgrade yesterday, I just restored the backup and have all my recent calls, etc. back, up to yesterday.
Also, if you have HandiTaskManager (which I highly recommend - have used it for three years now), you could access your log thru that program, since it's invoked by the center button, but I never did find another way to access the call log without it.
UPDATE: the damn thing just froze up completely...