Some movies start synced correctly but slowly drift out of sync. For these kind of movies you
can specify a delay factor that is applied to all timestamps -- no data is added or removed. So if you make that factor too big or too small you´ll get bad results.
An example is that an episode I transcoded was 0.2 seconds out of sync at the end of the movie which was 77340 frames long. At 29.97fps 0.2 seconds correspond to approx.  6 frames.
So I did
           $ mkvmerge -o goodsync.mkv -y 23456:0,77346/77340 outofsync.mkv

The result was fine.