Stabilize not applying correction to video?

I am having issues with Stabilize in Motion 5. I have added a couple of trackers and run the analysis and Motion generates the motion vectors on screen. However, when I play back it appears the motion vectors are not being applied to the video - the video shakes just as much as it did before, and you can see the motion tracking overlay still showing the motion vectors. Am I missing something obvious here? How do I actually get Stabilize to stop the shaking?

First of all, I must confess that I have not used Stabilize very much at all. It usually works great with the default: add + analyze (no trackers.)  So, I found one of the worst clips I could find and tried out various things with it and I have to admit, ***your problems are EASILY reproduceable***
PLUS, in Motion 5, once you get a bad track you will never get a good one!!! not in the same project no matter how many times you delete and re-add a Stabilize behavior.  On that bad test clip I used, I got a good track ONCE. Then I Added (not duplicated) a new copy of the same clip and tried using a tracker. The track is perfect, the playback just moves the entire video around like it's a Match Move on the track. Tried deleting the tracker; Analyze again, and it's stuck with the same movement that went with the tracker. Tried deleting the retiming cache (it's used for Optical flow and other motion things) and nothing.  [Meanwhile, rechecking the original perfectly stabilized *same* clip originally imported "new" — still perfectly stabilized — to add insult to injury, if I use the tracker data (that is, if I put the first clip in the drop well) from this clip in the 2nd import clip - the stabilization is exactly the same on the 2nd clip... which is completely pointless if you can't get the "right" stabilization to begin with!] [PS- by "perfectly" I mean it's the best possible stabilization I could hope for: most of the clip was rock solid, but high jitter/jerk areas still had some "blips" in it -- lined up fine -- but a quick re-scale kind of thing -- it was a really bad clip ]
Went into Motion 4. I didn't like the way Stabilize trackers worked for my test, deleted them, re-Analyzed with no tracker: WORKED PERFECTLY. No matter what I did to mess up the stabilization on purpose - I could always delete the trackers and re-Analyze without having to delete and replace the behavior - and start over again like I had just added the behavior. Motion 4 worked like you would expect it to.
So... I would have to say that Stabilize is YET ANOTHER BROKEN SOMETHING IN MOTION 5!
But back to your problem.  If you have Motion 4, use it to stabilize your video, export (as prores) and import into your Motion 5 project. If you don't have Motion 4... Open a brand new project; import your clip; Add Stabilize (NO TRACKERS); cross your fingers. If you get a good stabilization, export it out for future use.
By all means, let Apple know of this problem via the Provide Motion Feedback menu item under Motion.
Your specific questions: I would say if you have Motion 4, you could use the tracking region in that way, but I tried it in M5 and the Region is also a tracker and that will mess up the stabilization. If you only have M5, create a new project, import your clip, add the levels and adjust it for a "bit" more detail, add the Stabilize and Analyze only. You basically get one shot to get it right... per project per clip (maybe that's pushing it). Even in Motion 4, if the clip is in pretty bad shape, Stabilize does its best to get "most" of the clip right— so you may have to opt trimming out pieces that won't stabilize as well [in my experience, most often, that will be at the beginning and the end when you make contact with the camera to both start and stop recording, or to zoom.] You might also consider trimming the ends of the clip a bit beforehand as well because, no matter how you line up the clilp in the timeline, Motion analyzes the *entire clip*, no matter what!
Anybody else notice the lack of a Motion 5.0.2 update when FCPX 10.0.2 came out?? I'm still waiting. Every day I check— at least 3 times. M5 must be really badly damaged to be taking this long (and I have found A LOT of problems with it... most of which won't affect the average user... but stil!)

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