I am having the same frustrating problem. VERY ANNOYING!
I recently purchased the HT-C6900W along with a Samsung 8000 series 3D/LED/LCD television. I connected my cable set top box to the HT's HDMI Input 1 and the television HDMI Input 1 to the HT's HDMI Out. (As described on page 24 of the user manual).
When I turn on all three components (with my set top box programmable remote) the television remembers that input 1 was last selected however the HT-C6900W resets back to "D-In" after briefly displaying "HDMI.IN1". I must then grab the HT remote and select the correct source "HDMI.IN1" to view content from my set top box.
Is there some rational explanation for why Samsung chose to set the HT-C6900W to operate this way?
It seems utterly ridiculous to me that any device defaults to anything other than the last input used. It also seems equally ridiculous that "D-In" would have a higher precedence than "HDMI" in a system designed to support multiple A/V inputs. I can't imagine anyone who would buy a home theater in a box system (today) and not expect that HDMI would be the rule instead of the exception.
I would also expect that when a manufacturer (Samsung) develops products intended to work together (3D Home Theater Systems and Televisions) that this situation is avoided.
In my opinion, if the system can't be reprogrammed to default to the last used input, then the input order should be either configurable through the setup menu, or possibly the order could be HDMI.IN1 -> BD/DVD -> HDMI.IN2 ->, etc.
I don't believe that connecting an extra cable (Digital) between the set top box and the HT-C6900W and using 2 inputs on the television (one for the HT, one for the set top box) is a preferred solution.
If Samsung is watching this forum and if this is correctable via a software update, please consider a resolution. Other than this annoyance I am very pleased with the performance of both the television and the homt theater.