Lej1447,
Sorry, I didn't understand your original post until I read it again. I think you are correct that the pre/pro is recognizing the format that is output from the DVD player and breifly flashes that format on the display, then it goes into the mode that you have configured.
MY HT receiver does this too. Sometimes movie trailers or additional material on a DVD is encoded in DD 2.0 or some other format. I see my display change from DD 2.0 to DD 3/2/1, etc. as it goes from previews to the main feature. I think it is simply telling you what format is encoded on the disc at that time.
Your setup as you described it should be correct.
Enjoy,
TIC