NeoPhite,
any reason why you're not using the Motorola's DVI out to your HL-R's HDMI input? Using this connection will give you the best picture. Also, how is the video output on the Motorola STB setup? Your HL-R has a native display of 720p. I would set the STB for 720p and not 1080i.

While this is not about your video display, I'm a little unclear as why you're running the audio the way you are. From your description you are utilizing the Samsung HT receiver for audio. If so, this is what I would be doing.

If you use (and you should) the STB DVI out to your HL-R's HDMI you will need to run seperate audio cables since DVI doesn't carry audio. I would run component audio out from the STB to component audio in on the HT receiver. This would give you cable audio via your HT receiver. I would reserve the HT receiver's optical audio for the DVD player by running an optical audio out from the DVD player to the HT receiver's optical audio in.