elusian Ok, so I have read that there is an issue with conky: (segfault causes it to crash on startup).
I also encounter very very weird behaviour under GNOME X11 when running conky. Just wanna be sure if it's like the same thing you have described, or a whole other issue:
So basically I had only three programs running: chrome in multiple windows, gnome-terminal in multiple windows and rednotebook. Then I ran conky and could observe extremely strange behaviour:
normally, the conky "window" only gets displayed when hiding all windows, e.g. on an empty workspace.
But when switching workspaces after running conky, the conky "window" or how you call it got displayed on top of the running application.
I observed several scenarios:
a)by then pressing super+D, which should hide all windows, only the conky window got hidden and back on top of all windows by pressing super+D again.
b) another time, I couldn't switch between windows on the same worksapce. Either by pressing alt+tab and choosing another program or by opening overview and choosing another window on the same workspace did't show any effect. Didn't switch the active window.
c) I was on a workspace where only a gnome-terminal was running. But behind the gnome-terminal was the chrome-window shown, which was running on another worskace! By opening overview, I could see that there only was the terminal running on this workspace, but after closing overview, there was the terminal window, and behind it the chrome window. Though I did't test if I could interact with this background chrome window.
Even after killing conky, the chrome window from another workspace was shown behind the terminal window. Only after I switched to another workspace and the back, the chrome window from another workspace was gon and only the terminal window left.