I'm interested in how you do this too, so I wanted to join the thread so I can see how it works out..what suggestions you get...sorry I can't help with the problem you're having... I recently did a bunch of syncing mulitiple clips by a much less exact method.. which took forever... I am wishing you the best with resolving this well, regardless my personal inerest.
There is a really easy-to-follow explanation of it in Lynda.com. If I could just get it to work like the instructional demo!
The synch clips box just revealed the select "numbered clip marker" choice as selectable, and I think it was revealed because I just added a synch mark to one of the tracks that was missing one. I think if you don't have a marker on each track selected, it might default to start or end of clip only.
For instructions on how to do multi-track video editing, go to Lynda.com, premier pro CS4, beyond the basics.
I have to play around with that later...see if I can get it to work.
Thanks for letting me know what you did..