In Maestro, right click on the Untitled1 Project in top left hand window. You will see initial stream settings should be all unticked. You could actually try ticking Set Subtitles To and select OFF. Also, the line/window you loaded the Subs into, dont click the button to that lines left, if the button is Pink in colour then its the default Subtitle and it will be turned on.
I havent tried the latest Nero 6.3.0.x yet but it claims to have fixed the Video-DVD writting, what ever that means ?!?!?!?!
If I make a backup of a DVD5 using DVD DEcrypter in ISO mode and burn back with DVD Decrypter, my DVD Player will show subtitles when the movie plays but does not with the original. If I backup the same dvd but in FILE mode and burn with Nero 5.5 and I get no subtitles showing automatically, exactly as the original. So different burning programs can/does influence the playback.
As for RNM, ver 4.50 and 4.6x work quite well for me also but not for everyone. Nero 5.5 still has the best overall dvd player compatability as far as my experience goes.