Are your clips on different tracks or the same track? They must be on different tracks, e.g. Video 1, Video 2, and Video 3.
how do I get past this?
Just line them up manually. You're already done the hard part of finding the common point of reference for each clip.
I agree with Jim. I've done a lot of multicam projects and I've never used a Clip > Synchronize command. It should be a breeze to align the three camera angles on the timeline. If your magnetic toggle is activated the Markers will actually snap into alignment as you are adjusting their position on the timeline.
Or you could just set the in point of each clip at the clap marker, or any arbitrary equal distance from the clap marker, then overlay each of the clips on seperate tracks at the beggining of the sequence.
As long as each camera angle has a clear synching point and continuous video you should be golden.