Ok, I’ve figured it out, thanks to comparing two XMLs, just as you said!!!
The problem was that since I wanted to set up several synth plugins, I had used the same Control Names (like OSC1 Vol, LFO1 Rate etc.) several times. They were still assigned to different MIDI controllers and showed up in their own separate lines in the GR setup, but apparently this is something that messes up things. I could also see that in the XML - the respective tabs had two values assigned, which is probably the point where Cubase got confused. By giving each control unique names the problem could be solved, and everything is working beautifully now.
Thank you so much, Rhino - you saved me from a lot of pain and frustration!!! Two thumbs up! 