While I was searching for some option, I stumbled upon the "Configuration per file" window (under the "Run" tab in the menu, or via <Ctrl>-F6). The names of the sub windows are half hidden in my setup (I use KDE if that matters and I have adjusted the font size to something bigger than the default). See attachment for clarity. Paul
As far as I can tell this bug has been fixed in spyder 6 (or at least 6.1). The "Configuration per file" window has been restructured such that subwindows do not overlap. Please confirm if you're still experiencing the problem in spyder 6. Otherwise I think we can close this bug.