I have my Manjaro Cinnamon set to a light theme. But I updated the entire system today, and now, certain elements are in some dark theme, such as the “This program is not responding” pop-ups. How do I get those messages to obey my system theme again?
I replaced my terminal with the xfce-terminal because it allows me to work with multiple tabs, and to set background pics in my terminal.
When I opened a terminal as root, it used to show the background pic that I set in my root account. But as of late, after an update, the terminal opens the default gnome terminal again. Is there a way to get its original behavior back?
Cinnamon is based on Gnome - your set theme might have become unsupported by the upgraded version of Cinnamon.
Happens frequently with Gnome, so I’d suspect to see similar things with Cinnamon.
Switch to the default theme, disable extensions, check that the theme is indeed said to be compatible with the version of Cinnamon that you are now running.
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How do I disable extensions? I don’t even know what the default theme should be.
Or, more important, how to change the theme of those “log out now?” dialogues at all.
Can’t tell you of the top of my head … should be easy to find out.
But you set a different one - so you knew the place to do it. 
Those themes still look as I set them. And my entire desktop reflects that, except for those deeper-level messages, like “do you want to log out?” and “program … is not responding”.
Somehow, that theme seems to be defined somewhere else.
Can’t help because: can’t reproduce.
Can’t even try to reproduce because I don’t know what theme …
And what (global) theme are you using?
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This information (at least) might be helpful to those trying to help, don’t you think?