Maybe it is better to change the Ctrl+X in the IDE to Ctrl+Alt+X. Trying to solve a problem when I was aiming for Ctrl+Z in the IDE, two things had happened together. I was in the wrong tab and instead of Ctrl+Z I pressed Ctrl+X. It resulted in a deleted line that bugged me for sometime until I figured out what was wrong.
Yes. It does not only cut characters but also whole lines if you do it without selecting any characters. An alternative and more correct would be to point only the "Cut line" if no characters are selected to Ctrl+Alt+Delete.
Considering that this seems to be a very local problem, probably very near your computer, I'd like to instead suggest installing AutoHotkey and setting up a brand new hotkey for Ctrl-X that does nothing and one that is Ctrl+Alt+X that is cut. That would probably solve the problem for you.