According to what I can see, 00800.mpls contains the main movie, since its duration is 1:51:52. Is it what you have encoded? And 00300.ssif (in BDMV\STREAM\SSIF) must contain the whole movie in 3D (AVC and MVC streams interleaved together), or 00300.m2ts (in BDMV\STREAM) must contain also the whole movie, but only in 2D (AVC stream only). If it's not the case, either there are other SSIF files in the playlist and you have not copied their names here, or your MPLS is severly damaged.
I don't know if the simple fact of extracting the files from the ISO is sufficient to truncate the movie. That should not be the case. Either the structure is damaged and tsMuxeR may crash or refuse to work, or it is correct and it should work. But anyway, it is never a good ides to extract the SSIF files from a BD3D. As I wrote, that doesn't make sense.
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