Hello
I was having the same problem as others in this thread even with the new apple tv profile, ie, the apple tv wouldn't stay off (standby) when I either (from apple tv activity) pushed the off button on the remote or changed from apple tv activity to another activity. My harmony remote 525 set-up software didn't allow me to include the delays for the menu button and the select button as standard for power off.
I sent harmony a query using the method included in their software and they changed my profile to include the delays. I played dumb and didn't mention that I had read this thread just asked them to fix the not-turning-off issue. As mentioned they responded very quickly (within 24 hours) but it still didn't work. So I went into the software to see what they had done and they had added different buttons for power on and off and for the off had included 2 button process, menu for 2500 ms and 'play' for 5000 ms. I changed the 'play' to 'select' as mentioned above and it works perfectly now.
So it appears that the harmony set-up software (at least for the 525) doesn't
provide for the delay settings as standard and you have to request a fix from their tech support before they activate it.
I sent them back a response regarding the 'play' v 'select' issue and thanked them for their prompt attention.
If you are having the same problem and want the little light on the apple tv off when you are doing something else - contact harmony - explain to them that your apple tv won't turn off, say that it is a 2 step process, menu for 2 seconds and select for 5 seconds and once they update, (and if it doesn't work) go into the power settings and the delays should be there and change the button.
Cheers