The dark system theme I have set seems to make some applications look funny, with dark boxes where they should be light. Is there any way I can manually set a theme on a per-application basis?
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I dont know if this could be your issue, however I had some strange big black shadows arround GTK apps. After trying all different possible themes, playing arround with config files, CSS... Nothing helped.
However, on the Archlinux wiki, they mentioned something interesting:
The compositor.While this really depends what DE and what compositor is installed on your distro by default, I got rid off all the strangeness by enabling something in the compositor.