Some of the preset keyboard shortcuts in Mission Control conflict with those in FileMaker (specifically ctrl-up arrow and ctrl-down arrow). You should change those first. Also, be sure to select the new FileMaker version 12 when choosing the applciation in keyboard/application shortcuts..
No, this is not the well-documented issue with Mission Control Shortcuts. This is about going to the System Preferences, Keyboard Preferences and making custom application keyboard shortcuts.
To fix it, I had to remove FileMaker Pro Advanced 11 (or compress it to a zip archive and remove the original)and re-add the shortcuts. Though I was selecting FileMaker 12, likely because they have the same app signature, MacOS X chose FileMaker 11 each time. Now that version 11 gone, MacOS is choosing the correct version and works.
I'm going to file a bug with Apple now.
Were you not able to select FileMaker Pro Advanced 12 using the "other…" menu item instead of zipping and remvoing FileMaker Pro Advanced 11?
No, even when I removed all the shortcuts and the Filemaker entry from the shortcuts list, and went back and explicitly chose "Other" and chose FileMaker 12, it still only worked in FileMaker 11. As long as 11 and 12 were on the drive, it chose 11.
I presume this is due to the two apps having the same signature, and MacOS X just applies the shortcuts to the first one it finds.
I've raised the bug with Apple. We'll see what happens.