That's real odd… and actually by default <kbd>Ctrl+k</kbd> only *deletes* one or more lines, so it's not even related to clipboard. @toxpal could you try changing the key combination for the action (*Edit → Preferences → Keybindings → Editor → Delete current line(s)*) and see if it still happens with the new binding? My only guess for the moment would be that <kbd>Ctrl+k</kbd> is doing something at your desktop level as well.
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