Hi, you have to be Aware what the midi fader does: It sends midi channel volume control Messages (CC7). So your theory is correct. If the target Instrument reacts on cc7 it will do that on a per channel base. So if you have more than one midi channel in cubase using the same target channel number, you will always control the same Parameter on the target device on ALL These channels.
A solution would be to use different midi channels for different midi tracks. But of course this would have to be supported by the target Instrument as well.
Cheers, Ernst