So, I recently upgraded to 17.1 from 15.3 via 16.3... My preferred screenshot tool is Flameshot. But the native screenshot tool ALWAYS overrides Flameshot.
I set a custom keyboard shortcut for Flameshot... and the native one overrides it, takes the screenshot, and Flameshot sends an error. (Before you ask, there's NO equivalent shortcut for the native tool.)
In the system tray, I right click on Flameshot and say "take a screenshot"... and the native one takes the shot.
I right click again and say "open launcher"... and the native one takes the shot.
This would all be fine if the native one wasn't quite so basic. I am at my wit's end.
Did You tried to uninstall Flameshot and reinstall it? And do You use the Flatpak Version or the .deb Version? And did You set the Shortcut before Your Upgrade to 17.1 or before?
In an effort to try to patch things up with Wayland in order to force Wayland as the default protocol, Gnome had to replace the modular screenshot utility since Wayland cannot work with it and instead, incorporated the new screenshot tool into the Gnome Shell. It is no longer modular, so cannot easily be removed like normal software.
Will this terminal prompt get you the keybindings for the gnome screenshot utility? (I cannot test this at the moment, I am on my own system): gsettings list-recursively org.gnome.shell.keybindings | grep screenshot
If it does, unset the keyboard shortcuts it is using: gsettings set org.gnome.shell.keybindings screenshot "['']" gsettings set org.gnome.shell.keybindings screenshot-window "['']" gsettings set org.gnome.shell.keybindings screenshot-area "['']"
Once done, try opening the Settings > Keyboard Shortcuts and setting Flameshot to the shortcuts.