Blu Ray missing some scenes

[pepegot1]

I went to make a backup copy of my first Blu Ray disk and was successful to a point. I ripped with ANYDVDHD and found the m2ts files I needed. I used TSSlipter to put them togeher. I created the BDMV with TsMuxer. When I Play the result with VLC and it is good. However, when I played with Arcsoft Theater 3, the first few scenes were missing. This also happened with the burned disc. Why did I lose those few scenes and how can it be avoided?
When I burned the whole content of the ANYDVDHD rip, I got what I wanted minus the garbage-just the movie. Does ANYDVDHD just rip the main movie?
Also, is there a Blu Ray equivalent of ISObuster to repair a Blu Ray disc?
Please help-burning Blu ray can be expensive.

[Baldrick]

Load the playlist file with tsmuxer instead. Identify the playlist with bdinfo and then load the mpls in tsmuxer.

OR use an all-in-one blu-ray to blu-ray main movie instead like clown_bd or https://www.videohelp.com/tools/sections/blu-ray-to-blu-ray-avchd

[The-One]

I use Clown_BD to view the playlist and find the ones I want to keep then I use MultiAVCHD to blank all playlists I don't want. If you just want the main movie only, as Baldrick suggested, use tsmuxer and load the playlist then then output to BluRay. I don't like to use Clown_BD to blank playlists because it breaks the disc navigation many times.

I like to use TotalMedia Theatre to preview BluRays before burning because if they don't play right with TMT, then they usually won't play in a stand alone player....as you found out.