Ok, here’s an update on where I got with this.
Issue 1 - Steinberg support suggested not to import old projects or templates from C6x. You need to recreate all your templates. To all my friends with orchestral or VSL templates, this sucks balls, unless you think that hours of setting up templates is ‘fun’.
(given my next points this might not be the case always. As you’ll see, I think the issue was that the CMCs were only talking to the first 16 channels and since I placed all my inputs first, i never got the CMC FD to find the group channels - see my workaround)
Issue 2. The CMC FD still does not appear to talk to Input channels or Output channels, but it will talk to Audio, FX, Midi, Group, Folder and VST channel types.
Issue 3. The CMC FD under Cubase 6x only addresses faders in Mixer 1. Under C7, it addresses channels in Mixer 1,2 & 3 simultaneously. (so my old approach of setting mixer 1 to display ONLY Group channels is no longer valid)
The workaround I am now trying, besides creating all new templates, is to put 16 group channels at the top of my Project Track List (therefore these will always be the leftmost channel faders). This way as new tracks are added, they will not reassign my group faders from the CMC.
I also tried this will 12 Stereo Group faders and 4 FX faders and that seems to be working ok too.
Doing this allows me to keep three Mixer windows on my second monitor, top being my tracks (Mixer3) Lower left being my inputs (Mixer2) and lower right being my Group faders (Mixer1), with the studio Control Room wedged in there too.
So if you want to lock the FD faders to specific channels, make them the top of the project track list.
I can appreciate that not everyone wants to work this way and the CMC FDs are designed to allow you to nudge/jump back and forth across track channels, but I have wired up my studio so that subgroups to go out of my DAW and get summed in the analog domain - thus I want those faders tied to controlling the output level of my sub groups.
Hope this saves someone some frustration…