Do you have your TV muted? I used to run the HDMI direct to my TV and the sound to my pre/pro. If I forgot to mute my TV the timing in the sound from my TV did not match that coming from my HT system and it made it very difficult to understand. While you wrote that only the video is being sent via the HDMI to the TV, I would double check this. Since you indicate that this only happens with videos (vs. music only), it may be the cause.
Outside of this, it would seem it would be a set-up issue. If I am correct, you have run the full set-up, speaker placement/distances, etc. . . from the DVD player and during set-up the test signals all worked well?
I just keep going back in my mind to the dual outputs using the HDMI and the analog 5.1 channel output. Since it is not your HT receiver that is decoding anything (ie. based on the analog input approach and assuming you haven't programmed the Denon to do any changes to the analog signal).
I don't think my DVD player (Oppo) allows me to restrict the HDMI output to just video, but I may be mistaken.