I spoke to an Apple support guy about this issue yesterday. He walked me through using a reboot while hitting Command-Option-p-r. Made no difference unfortunately. However I did send him a link to this thread via email.
I upgraded to Lion as a desperate attempt to resolve the issue but that made no difference either.
What I have noticed is that you can set the brightness OK in native iMac mode, then when you swap to external display mode it bascally resets the brightness to max and F1 and F2 have no effect, then if you go back to native iMac, it remains at max.... so I have to wind it down again.
I know this is not the support guys fault so I'm not mad at him, but he did basically say that if the hardware I'm using isn't entirely Apple (ie my Lenovo laptop and Monoprice Displayport-to-miniDisplayPort cable) they are unlikely to take my support case very seriously. Really?? The fact that it USED to work just fine with that hardware, but 10.6.8 brought me tan-while-you-type brightness levels isn't proof enough?
Also, after I mentioned this forum post, it doesn't sound like Apple take it very seriously. Don't expect Apple support to be scanning the discussion forum... I don't think they are.
And if they are.... APPLE!! Please treat this VERY REAL problem with TOP priority and fix the f$%king thing! If you can't be bothered, send me the **** code and I'll fix it.