If you want to synchronize and JOIN two subtitle files into one file follow those few steps:
1) Synchronize 2 subtitle files separately (do not join it in a first place!). First synchronize the first subtitle file and the load movie again, seek to the middle of movie and synchronize the second subtitle file.
2) You should finish first step with 2 subtitle files - first file should fit fine first 50% of move and the second file when loaded should fit fine second 50% of move.
3) Then join both subtitles.
You should press the button in player when subtitle line should appear (usually when the person starts to say the line).
Let me know if this works fine