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Some xkb mappings have the non-breaking space assigned to a combination of key (for instance AltGr-Space or AltGr-Shift-Space). Some compose database also have a mapping (Compose space space for instance). You may be hitting one of those involuntarily.
Indeed, Geany is having an option to insert an alternative space. You can find the option inside the "Insert" menu and/or you can set a keybidng for it (inside the insert section of keybedings). In default there should be no keybinding set for.
As others have mentioned it's likely to a specific service or process, which you should be able to kill. You can start gnome-system-monitor as root to see all of the processes on the system and their CPU load. Instead of rebooting next time try a few things: Use the CTRL+ALT+F1 through F7 to switch to another terminal. This will cause your X graphics ...
IMO, You need to identify the service which you want to restart(use "top" command for the same). You will have to be cautious while choosing a service to restart. For an ex: top will also list "firefox" so you should refrain from killing it as you do not want to close it.
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