I had something similar a little while ago, I booted from a 10.3 disk (the PB had been updated to 10.3.7/8 + firmware etc). The airport didn't work of the other disk and when I booted off the internal drive the airport wasn't coming up at all.
It recognised that it was there in the profile, but couldn't use it. I restarted etc, disk permissions, ran Onyx to wipe everything (caches etc - not the disk) and for some reason it came back. It was an unerving experience.
I don't have a solution really, but mine came back - I didn't open the computer up or anything.
Try making a new user and using that account (as suggested above), I think airport may work outside of the user preferences though. Run Onyx or similar to clear cache files - something may have become corrupted, maybe.
Not much help, sorry