When you run multiple instances of Gnome owned by the same user, it is expected the they share the same settings. That is, the choice user made for the desktop background is applied to all the running instances of Gnome.
About the first desktop losing the control, it looks less normal and seems to be a problem in Gnome, triggered when multiple desktops share the same configuration files.
If I understand correctly, you need multiple desktops each with its own, indepedent configuration. In my opinion having more users is better for you than sharing a single user account across more desktops.