I am using the Mocha pro v4 but still using CS5.5 as I see no reasons to get CC. But I did have this same problem and have not yet heard from Imagineer. I have 4 masks that are are linked to one master track. Everything looks perfect in Mocha Pro. But when I import into AE the first frame shows one mask, by the 2nd frame the 1st mask disappears and then another mask shows up for a while then disappears, then a new set of masks show up.
What I did notice was that on certain tracks, which had some manual keyframing, the blinking of the frames in AE coincided perfectly with the frames those keyframes were on. I really dont want to have to buy another adobe product! Such a PITA converting all the plugins over. Uggg. There has to be another way.