I've been sent an animated graphic with alpha channel as a Quicktime Pro Res movie. How do I import this, keeping the alpha channel? I've tried 'invert", "do not invert"and "ignore" in the Import settings dialogue box. Each option results in the same, a normal clip that does not key over a lower video track. 

Do you have Photoshop?

If so you could try opening the movie in Photoshop
Exporting the movie from Photoshop as an image sequence selecting the appropriate alpha information.
Import image sequence into MC.  

Worked here with non alpha ProRes .mov  (sorry no alpha .mov to test with readily available)

If you have access to After Effects you can use this guide to export as DNxHD with Alpha Channel and then Fast Import:

Importing DNxHD with Alpha from After Affects

Keith