Changing sample rates in a multipart system always risks causing a brief noise burst and should not be done lightly. It takes a short but finite time for different parts of this complex system to detect the change and to react to it, usually by muting until the system becomes stable. This is pretty much unavoidable. Sorry.
Don't know why the Cubase is changing the sample rate – this is beyond our control.
The erroneous 96kHz indication on the control panel is a reported bug which will be fixed in the next release.
Not quite sure what you mean by routing the FireWire output to the ADAT output. You can certainly drive them with the same source, but outputs cannot be connected to each other.