Thanks for clarifying, I haven't thought about this for a few years and can't believe it's still not resolved. Like I mentioned, I've been suggesting turning off HDMI-CEC for 3 years. I thought that ARC would be the lever to get manufacturers to set aside a register or one memory location to save a startup input before shutting down.
Your equipment is similar to my two friends' with Samsung TVs, Comcast cableboxes, and HT-C6600s. A Harmony 650 remote (that can control 5 devices) solved the problem. I've seen it as low as $50. Both have Anynet turned off in the TV and HT. One friend took the remote out of the box, carefully followed instructions and set up Watch TV and Watch Movie activities. His works perfectly.
The other screwed around with his 650, couldn't get it to work (see my link referenced above) and, while I should have just reset his 650, I was drawn in and forgot about that, but managed to add a command in Watch Movie before it shuts down to change the input back to HDMI1 for his cablebox when he powers back up .
So I suggest trying a Harmony capable of handling the number of devices you have, reading instructions, and carefully setting it up. Good luck.
Also, does anyone know if newer models of Samsung HTs have resolved this issue, possibly with firmware updates?