garageCube

I have 2 quads, the second over laps the first. I have been trying to mask the second, so you can see movement behind the image in the second quad. This is how I do it.

I select quad 2 and then drop down and select mask from the Visual box. I then create my mask and I now can see the movement happening below Quad 2. The problem is; when I come back to this cue, the mask is no longer there. I have tried changing different options under Inspector=> Visual but none of them seem to save my masks. What am I doing wrong?

I can't reproduce this issue. Did you create the mask before creating the Scene or Cue ? If not that's the normal behavior. The mask settings and geometry are stored in the scenes & cues by default. But you can update the geometry of your mask in all scenes & cues at once.
To do so: select all scenes & cues, press the "Edit" button in cue toolbar (or menu Cues / Edit Cues...), select your surface and press the "Mask" button. It will update the mask setting of this surface in all scenes & cues.