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When playing a radio channel from the Freebox, the proper audio stream is not selected (multiple streams, one per radio channel, embedded into a single multiplex): the first stream is always selected.
Also the video channel is enabled (behavior differs from version 1.1.11)

What do you mean, not selected?

When using the Freebox, the user can select the service to play by selecting its name into the list of available programs.
In the case of audio channels, multiple (say 6 for exemple) independent radio channels are carried (multiplexed) into a single service (transport stream).
Playing a given radio channel, implies reading the proper transport stream and demultiplex the proper elementrary audio stream (track, pid ... ... whatever name you use).
The "France Musiques" program, for exemple, should read a given transport stream and demultiplex the 5th elementary stream (audio track, pid...).
For all the radio programs you try to play, the audio track selected is always the 1st one.
The audio track information is not used by VLC 2.0 (you have to manually try and select each audio track using the audio menu until you hear the channel you wanted to play).
Previous versions (the last one I used was VLC 1.1.11) were correctly taking this information into account to select (demultiplex) the proper audio channel.
I hope it's clear enough

Of course, it is selecting the first program when you give a TS. I don't get how it could guess which channel you want.
I must miss something or you are not clear. Are you using a playlist?

The information (TS+ES) is provided by each entry of the playlist (CTRL-L => Internet => Freebox).
I don't know how it is encoded but when I query the information for the entry, I see that all entries that are carried by the same TS, show the same stream info
(for exemple: emplacement "rtsp://mafreebox.freebox.fr/fbxtv_pub/stream?namespace=1&service=100006")
but differ by the "Artiste" information (for exemple artiste 10003 for "France Inter" and artiste 10018 for "France Musiques")

This "artiste" information must somehow encode (ou lead to the ES) because I hear "France Inter" on track 1 and "France Musiques" in track 5.
Querying the codec information gives further information about the original id (pid?):
France Inter => Artiste 10003 Original id 1001 on track 1
France Musiques => Artiste 10018 Original id 1006 on track 5

I repeat that when asking "France Musiques" I hear "France Inter" (audio track 1 original id 1001) ... Selecting (audio track 5 original id 1006) plays "France Musiques": the track information is lost somewhere in the process (or not properly extracted from the entry information).

This was working as expected in version VLC 1.1.11 ...

Grumbl... How are you opening the stream? Are you using a playlist?

Yes as I told you above (CTRL-L => Internet => Freebox)
The broadcaster did choose to multiplex independent audio programs as elementary streams carried by a single transport stream (for efficiency reasons i suppose): 6 audio es per ts.
He is also providing the associated service list (requested to the freebox and shown to the user via CTRL-L => Internet => Freebox) to allow the user to play each program by selecting its name.
To this end, each entry (a program name) of this list contains enough information to properly demultiplex the proper elementary stream (audio track in this case).
This information appears to be encoded into the "Artist" field.
This playlist and the way to handle it may be specific to the "Free" Internet Access Provider (triple play : Internet, TV, Phone).

This was done by the previous versions of VLC without any special configuation (this is a specific extension for the french "Freebox" set top box).

VLC 2.0 seems to ignore the "Artist" information and always plays the first (default ?) audio track. The user has to try selecting among the 6 audio tracks of the ts until it hears the program he selected initially in the list.

Were you able to spot the problem (Freebox specific Playlist handling) ?
Can you give the status of this problem ?
Thanks