I had a very similar problem with FCPX 1.0.4. I recorded a jazz concert with 3 cameras. 2 of the 3 cameras were stopped when they had a prize give-away on the stage before the last song. When sync’ing, the last 2 clips from those cameras were joined with the beginning clips.
The only way I could solve the problem was to break the long clip into 2, then sync the 1st portion of the concert, then the final. Worked perfect that way.
However, I did a wedding last weekend with 3 cameras, and as of last night, I can’t get any audio sync to work at all. I ingested media into FCP X telling it to create proxy and to analyze audio. This is the first time I have ingested thru FCP X. Normally I ingest thru iMovie, then use mPEG Streamclip to convert to ProRes, then import those files into FCP X. I may try that and see what results I get.