I've tried it connected through HDMI and Displayport. Had the same issue on both. Tried different monitors which had different resolutions too...
BUT! I've done some more investigation and figured out a solution:
1, It doesn't occur when you have your game window at a fixed pixel resolution, only when you use free aspect (or any other aspect ratio fixed viewport rather than fixed pixel).
2, It is definitely the canvas resizing - see this
video which shows scene view and the canvas growing when the playmaker window is on the second screen.
3, It seems to be resolution dependant. If you have the main screen on the retina display and the playmaker editor on the 1080p display then the canvas gets smaller. If you have the opposite (PM on 1080p and main window on retina) the canvas gets bigger.
This points towards something funny happening with rendering the playmaker editor window at different resolutions effecting the size of the uGUI Canvas. So...
You can set apps to open in 'low resolution' mode on a retina MBP:
Hooray! This completely fixed the flickering!Issue fixed but it's a little worrying that Playmaker seems to do odd things to Unity on high resolution displays...