Pre fade insert vs post fade insert ! Aux prefader where as master track is post fader insert. Try pro L on actual Master track in pro tools. Same result? Also, you can try multing ( control clicking / Windows start I think I'm on Mac ) which is sending output to multiple places. Also doing this can help your Master fader provide an extra layer of control. The Master will show a plus symbol on its I/o drop down if done correct. I usually route to an aux named mixbus, which feeds my print track, with a Master Fader.
I have to say I just tried pro l on my mixbus ( aux insert / pre fade ) which is routed to stereo audio track with no plugs and no clipping or red. I then put the pro l on actual master track ( post fade ) and again no clipping or red lights on print track!
* in pt 12.1 and on you can also do the multing in the I/o setup dialog window.
This multing is important if printing stems of a mix with bus compression, so the stems who played together exhibit the same mix as the compressed 2 mix.
I have experienced same issues you describe before when I had double routed or not had my routing fine tuned in my session

hope this helped