I'm very confused.
Unless there's a new method in CS6 I'm just not aware of, you can only "sync" multicam clips in a sequence. That's the only place that allows you to see all clips at the same time and align them up so they match.
So...I'm not fully understanding what it is you're doing in the "left-hand window" (Source Monitor?, Media Browser?, media Bin?)
Hmmm. Well, I imported each video clip into the Media Bin, then screened them one-by-one in the Source Monitor. At the appropriate mark-in spot, I set a Mark In on each clip.
Next, I highlight all three clips simultaneously in the Media Bin, then right-click to choose "Create Multi-Cam Sequence." And I select "Marker Point." Premiere then creates a new clip in the Media Bin, renamed "Clip1MutliCam" (for example). I click on THAT clip and all 3 angles appear in the Source Window.
My problem arises when I start adding Mark In & Mark Out to the Multicam Clip so I can add footage to the Timeline. The audio goes out of sync in the Source Monitor... But the same footage, when placed on the Timeline, has synced audio once again. So the issue is in the Source Window only.
Sorry for not explaining that one better. I haven't tried syncing clips in a sequence. Again, I'm just a novice at this... My method seemed very similar to how Liquid does MultiCam, so I assumed it would work in similar fashion.
OK, I get it now.
Instead of loading the new multicam sequence in the Source Monitor, drag it down to the New Item button. This will create a second sequence with the milticam sequence nested into it. From there, go to the Window menu and open up the Multicam Monitor. Do your editing from there.