Question:
I open Innertube, before opening bioexplorer and the space ship will automatically fly (before I have pressed play in BioExplorer). If I close Innertube and reopen it, the space ship still flies automatically. If I close BioExplorer and Innertube, then reopen them both, the spaceship still automatically flies. If I shut-down and restart the entire computer, the spaceship still flies by itself. Eventually (and I don’t understand why), if I do this closing down and reopening enough times the spaceship will finally link back in with BioExplorer and function normally.

Answer:
Inner Tube is connecting to another BioExplorer over your network. It has the capability to receive data from a computer over a network.
 
When it is not working it has connected to BioExplorer running the SomaticVision.bxd design on another computer in your lab.

The quick fix is to simply disconnect your network cable from the computer, (and turn off your wi-fi). Then close are open inner tube to reset the connection.

The complicated fix is to open the Inner tube Measurements Window and verify which server it has connected to. I assume that it will choose the local server over the remote server as long as BioExplorer is open on your computer first. So make sure to open BioExplorer locally, then open the SV design, then open Inner Tube, to make sure it chooses your local computer.
 
There is also a "server selection drop-down" in the BioExplorer Measurements Window. When you have BioExplorer open on your local computer, as well as on a remote computer. If you have the choice of 127.0.0.1 or "localhost" that is your local computer, anything else is probably a remote computer. To force BioExplorer to connect to your local computer, type 127.0.0.1 (I believe, or if not try "localhost") into the server connection window.