In Known Issues and Solutions (several months ago) there was a workaround posted for something similar. Now, the issue isn’t exactly as you have described yours, but it might be worth investigating, nonetheless.
It’s a longshot, and will not necessarilly solve the issue.
In KDE Plasma there is an option to “Start with an empty session” which worked around another similar issue.
Not being a Gnome user, I can’t say whether something similar might be helpful in Gnome.
Regards.