I saw a locked thread about this in the Collected Issues but with no answer.
I had the same issue in Cubase 6 and am wondering if I am just doing something wrong.
When I open a Project, I usually have to reset my Control Room to my setup.
For instance, I send the Mix to Cue 1, Enable the Talkback to all the Cues, Route the Click to Cue 4 etc…
The Basic configuration is always still there.
Talkback inserts and my Speaker outs tend to stay correct.
Is it just me?
If you save your controlroom setup onemore time under the name “Default” (notice the capital “D”, it’s important),
things will go better. However, if you start cubase, and open a project with a different ( older) controlroom or vstout configuration right away sometimes things " change". Opening one of your " known good working files" first may help.
Same thing works for other ( vst) config files. Also you can try activating " use exclusive in/out ports for controlroom " or something similar in preferences. I have several config files named as I like, and I just recall one, then save it as Default. This way usualy everything stays the same until I want to change.
I did some testing, on my laptop I only have one stereo output when using the onbord soundcard. When using the controlroom, I have to save the VST connection “output” tab as default with NOTHING connected, and ALSO the “controlroom” routed to my soundcard as default for this to work. otherwise (with a faulty default-setting in the “output” tab, connected to my soundcard) the controlroom is disconnected everytime I restart Cubase.