If anyone is interested in this on the Firefox team - I found I can make shortcuts work by pressing the Fn key at the same time (so Fn-Cmd-T for a new tab). I tried Beta and Aurora and the same thing occurs on both of those. It's a bit annoying but I guess I'll get used to it.

One more thing, pressing a Cmd-X style keyboard shortcut in Thunderbird causes a crash - I can't see a way of sending the crash report to Mozilla but I see this line in the Apple report:

• • • Terminating app due to uncaught exception 'NSInternalInconsistencyException', reason: 'Failed to get CharCodes from EventRef (-9870)'

Can you switch the functions around so that the software functions are the defaults and no longer need the Fn key? That would be done from Sytem Preferences > Keyboard.

That didn't change it. The option

"Use all F1, F2, etc. keys as standard function keys"

was unticked, I ticked it and it still acts the same with shortcuts not working. Thanks for the help.

Sorry, my fault. I use a program called Ukulele to create a custom keymap that matches my physical keyboard. It seems under Lion it causes a few side effects in different programs - it's the most noticeable in Firefox and Thunderbird. I've gone back to the standard input and everything is working.