Adding my experience with this bug. Here is what happened with me and what I had to do to fix it:
Shot inverview & B-roll on 2 cams; a T3i and a Canon HardDrive camcorder as well as external audio via a H4n. Imported from SD card reader & camcorder's HD via USB to a single event. Analize for stabilization & rolling shutter was unchecked (as I usually do). For information sake; I was also working in "Original/Optimized" media.
After import was finished, I went though the footage, syncing audio (through FCPX's audio sync tool) and then creating mulicam clips of the interview-portion of the shoot with the newly-synced clips. So far so good. While I was doing this, I tried stabilizing the one camera (angle) from inside the angle editor. Noticed it was working for the first clip. Cool. Never tried that before, looks like it will work. I'll save that step for the finishing process.
Put together my rought cut. Pick my angles on the multi-cam clips. Satisfied, I pull over some B-roll on top of my storyline. Looks pretty shakey, so I select the clip and head to the inspector to see if I can stabilze it a bit.
What the... there is no stabilization or rolling shutter options? That can't be right. I try another b-roll clip from my Event. No. Nothing there either. Weird. Is it something to do with multicam? Does it disable the stabilization function? I go back to my first multicam clip in my storyline (the same one that I first tested to see if I could stabilize a multicam clip) I open it up in the angle editor and click on the clip. Sure enough, the stablization option is there. I try click on a differant multicam clip, the next one placed in my timeline. No stabilization.
The ****?
I systematically go through all my event clips. Long story short: I can only get the stabilization option to appear in the inspector window on a select few clips. Chronologically, only the first one or two that I imported from the T3i and none from camcorder. The rest will NOT show the option.
After checking out online (here) I try some of the helpful options. I basically tried everything suggested (relinking media, delete prefs, open in timeline, right-click analize & fix, ect). The only thing I didn't do is re-install FCPX because I didn't get that far.
In the end, what fixed it was creating a new Event and re-importing my footage, which is a major pain given that I already did all the work of organizing, syncing and creating multiclips. However, I did NOT reimport from the camera/card... I imported out of the original media folder in my FCPX Events folder on my computer. Then, I was able to manually grab and drop the clips from the new "02" event onto the original project. Magically, the stabalization option has returned on those clips from the "02" event.
So... this is definately a bizarre bug on the FCPX side, possibley during import. I would believe it was a camera-issue if it wasn't for the fact that re-importing the exact same files FROM THE FCPX EVENTS FOLDER fixed the issue. Right now, my project is referencing duplicate files from two events, the original that won't allow stabilization on certain clips, for no apparent reason. And the "02" Event that re-imported the same Original Files folder from the first Event. Waste of space and messy, but I did not want to loose editing time to start over from scratch. Later on, I will attempt to consolidate the files via the project-duplication tool and see if it keeps the stabilization option on the clips that need it, then trash the dupes.
I would also have suspected muticam or audio sync was causing, but I was able to drop in the clips from the "02" event inside the angle editor (super handy, btw) and the stablization came back. I even clicked back and forth between the two, identical clips in the same viewer, watching the stablization option appear and disappear, for no apparent reason.
It may also have something to do with the mixing of fps. The project was in 29.9fps (matching the camcorder files) while the T3i was shot at 24p. But I would believe that more if it weren't for the fact that the new Event import with the exact same frame rates on the exact same files fixed the issue.
Anyway, good luck. And please fix this, Apple. I've always had faith in you.