You will have to isolate to see if it can be fixed via software or if you will need to replace the keyboard.
Right off the bat, boot to your install DVD or to Lion Recovery, depending on which OS is installed.
In the install volume, select Utilities > Terminal.
In Terminal's window, test the comma key. Does it work?
If not, you can try removing and re-pairing the bluetooth keyboard, but if it still doesn't work, you will have to replace it.
If it does work, then it is your software, and further isolation is necessary.
From here, I would test a new user. I would wager that the issue is going to be user specific if it is isolated to the software, but you should double-check with this step.
If it is in fact user specific, meaning that it only happens in your user, then enable the keyboard viewer in Sys Prefs > Language & Text > Input. Open the keyboard and press the comma key. Does the software keyboard show that it is detecting the comma key being depressed?