OK, did a little detective work.
It seems after you start up the PS3 that it still asks you to press the PS button to connect a controller. Shouldn't the PRO be paired already. I only ask, because I've paid a little more attention to the actions of the controller. It would see that, if you don't use the PRO for some time that it becomes un-synched to the Slim. Example, start up PS3, start game play game for extended period of time, exit game and go to navigate the XMB with the PRO. The first button press has major delay. It would appear as the PRO is resyching with the PS3. This would explain the power off macro failure. Each time it fails, it fails because it doesn't register the PS button press at the beginning.
Therefore it would appear that first PS resynchs the PRO, but then it leaves the up, down, "X" commands to be executed in what ever menu you are in.
This may be why it doesn't occur all the time for me, only the times that it loses synch?
Have you guys run into any issues yet. I know you were looking into it.