The 16:9 flag is added as part of the MPEG2 encoding paramaters. It does not take it from the QT reference or file. Look in your settings for the MPEG2 and there should be an aspect ratio setting of either 4:3 or 16:9.
That audio message can also mean an issue with the graphics card. Make sure it is a supported card and load the drivers from the Avid utilities folder.
What video format are you playing? Are the drives fast enough to play them? Do you have any color indioators in the timeline after playing in those sections?