A couple of things, snow leopard, from what I hear, has had a lot of bugs. (especially with installs) A problem may be that you archived and reinstalled instead of just doing a clean install...? If that is the case then I would suggest a fresh erase and install. This will clear the hardware assignment stacks and allow you to map the keyboard properly (at least in theory).
If this does not work then there may be a hardware problem to blame. That does not seem likely, but cannot be ruled out just yet...
Had to reinstall 10.6.2 on IMac after erasing disk for an earlier problem with Adobe CS4 installation. The Adobe Tech Support could offer no help with all log files submitted and as a last resort suggested I erase the internal drive and reinstall system and applications. It worked.
Two problems encountered so far are : Inability to assign F13 key "to look up dictionary" (default being command -control-D) and the F11 and F12 keys no longer control sound volume as they all did before the reinstallation. I am unable to assign the keys in the System Preferences as suggested by Apple.