Can you specify how Mercury Transmit is not working in this configuration? Is there no output, wrong output, or something else? Screen shots or a photo of the two monitors may be helpful.
Does it make a difference which monitor the menu bar is attached to?
You stated that this works if the displays are arranged side-by-side. Does it make a difference if the MacBook Retina display is arranged above the external display instead of below it?
By "not working" I mean Mercury Transmit does not appear at all.
I tried the 4 combinations of above/below + menu bar/no menu bar, adjusting the Mercury Transmit Preferences when needed.
The only vertical arrangement where Mercury Transmit will show is the following:
This doesn't reflect my physical workspace, however.
Thanks for the additional details. I'll see if I can replicate this configuration.
One thing to check: make sure the After Effects application frame does not extend onto the monitor you want to use for video preview. Floating panels are OK, but if the main UI frame is on the monitor, it can not be used by Mercury Transmit.
2 positions (top or bottom) * menu bar position * Transmit which Display = 8 combinations
Of these eight, only two work: Arrangement 1 and Arrangement 5
Arrangement 1 is bad because I am transmitting to the external monitor which has poor colour gamut.
Arrangement 5 is bad because the screens are placed inverted to their physical positions; I have to travel upwards to go to the bottom screen.
Arrangement 7 is the target.
The picture at the bottom is the limit when Mercury Transmit will stop working. If I move the lower screen any further to the right, Mercury will stop.