Going back a couple of months, a contributor here, Ed Macke posted this THREAD, indicating a problem with Track Matte Keying in PrE. It worked well for him, until he did other editing, and then it would not work in that Project again. I tested it, in a Project that Track Matte Keying had been added to, early on. Ed was correct. When I went to add it again, further along the Timeline, it would not work - the Matte was treated just like regular Video (like a Title), regardless of how I tried to link to it with the Effect. We moved to other Video Tracks, cleared all Media Caches, did everything that we could think of, but it failed for each of us. Now, the earlier applied Track Matte Keying functioned, just as it had, when I did it in this test Project. The Effect worked multiple times in New Projects for each of us. We never were able to isolate any exact cause. It almost seemed to be time, or keystroke sensitive, as odd as that sounds. Projects just seemed to reach some point, after which Track Matte Keying would fail, even though totally different editing operations had been performed by each of us. We both filed the best Bug report that we could put together, to help the Adobe techs replicate it, but there seemed to be so many variables, that I'm not sure how well they were able to replicate and test. To me, it was just do a bunch of "stuff," and after a point, the Effect would just not take. I never heard anything from Adobe.
I was using PrE 4, and IIRC, Ed was on PrE 7, so it was not one particular version. I wish that I had some "cure," or at least an "avoid doing ____," but I do not. It seems to be a Bug, but we never were able to figure out the "trigger." The best that I can offer is to do nothing but cuts on the source footage in a New Project. Then, add the Track Matte Keying. Afterwards, finish the editing with things like Transitions, and Audio editing. Do not Render at any point, until the Track Matte Keying has been successfully applied, as it seemed that Rendering might have been one of the triggers, but certainly not the only one.
BTW - PrPro does not seem to suffer from this Bug, in any version that I have owned, or read of.
Sorry for the bad news, and I only hope that Adobe can track this down, and find a "cure."