The only time I ever had this issue was with a downloaded AVI file. I managed to extract the audio from the file, split/convert into 5 mono wav streams with Tranzcode (free) & re-assemble to DD 5.1 with Sonic Scenarist & them merged the 5.1 audio back.
To do it with a DVD you might have to extract the mpeg & them demux with something like TmpGenc & then do as I did & merge the 5.1 into the demuxed mpg & re-author. Not too complicated I guess but I don't know any free software to do that.
There might be some guidance available on www.videohelp.com