I think your Routing issues result from a misunderstanding – when you select the preset on the Routing program, this downloads the values to the unit. It does NOT load the routing preset on the H8000. You should look at the Input,Output,DSP A and B pages under SETUP and make sure the correct changes have been made.
I'm going to have to assume that your Cubase issues are unrelated to the Routing ones. You are right that when in Internal the H8000 ignores other clocks. Less so about slaving to Cubase – you can't do this. Either Cubase is slaved to the H8000, or it should be slaved to some other device to which the H8000 is also slaved.
But, Cubase can change the system sample rate – under ASIO there is usually a setting for this. This is what seems to be happening – but it's hard for me to know why. You may have to ask the nice Germans about this.