I have taken a closer look to the (new) mpls file with BDedit: Obviously TsMuxer is messing something up! As you can see in the picture, compared the two (original and new) mpls file of the main movie: the new one is lacking some information!! Especially the "subpath" type "IG Menu" section is missing. I think that this is the link to the pop-up menu!
[B]Original[\B]
[B]New[\B]
How can I prevent tsmuxer from ignoring this information?