Ok, good. That shows you have additional (mpls) playlist files, so it might just be that MC is not correctly detecting these.
To make this case, it would be helpful for you to download the MediaInfo tool:
http://mediaarea.net/en/MediaInfo/Download
and use it to examine the contents of each of those mpls files. If you can capture this, zip it, and post it, I'll take a look. There is both a GUI and command line interface. I don't recall how the GUI works, but you'd want to save the info as some form of text file. Via the command line, you can open a Windows CMD shell (Start menu > and enter "cmd"), and then you can run:
cd Desktop
and then run:
mediainfo --full D:\path\to\BDMV\PLAYLIST\00001.mpls > 00001.txt
etc, but using the correct path and correct playlist name, and changing the name of the .txt file each run to match the name of the mpls. Then archive those files into a zip and attach to a reply here.