@gonca
OMG... Not everyone is a criminal, get your mind out of the gutter!
@AmigaFuture
Thanks for your response, I know about MKVMerge but:
I just backed up the disk and realised that the 5.1 audio was set to default (I want the stereo track as default). You can only set default tracks in MOVIE-ONLY mode which I forgot to do, so I want BD-Rebuilder to rearrange the Audio Tracks without having to re-encode the movie again (I have a old machine, it takes about 6-8 hours for Highest Quality backup).
BD_RB is an "all-in-one" application and everything that I have read so far leads me to believe that it should do what I want (unless, as i said, there is a valid reason why its not allowing this to happen).There should not be any reason to start messing with other tools
P.S. I just remuxed with tsmuxer to put the stereo track first, as a workaround; but I thought I should report a potential bug...