I have a Mac app called Palua that automatically switches between the Macs FN keys (brightness, music controls....) and the F1-F12 keys whenever a certain app is open. I had it set to switch to F1-F12 keys when Minecraft.app was open, and this worked fine with the old launcher.

With the new launcher, this does not work anymore, because the game does not load in the launcher window, it opens in a new window called Minecraft 1.6 instead. So Palua does not recognize the newly opened minecraft 1.6 window to switch to F1-F12 mode.

Here is the app: https://itunes.apple.com/en/app/palua/id431494195?mt=12