O.P. RE: CTRL+D not working system-wide when text formatting shortcuts are enabled
Yesterday, switching this option on/off was definitely having an effect on the CTRL+D combination. I observed it multiple times. But today it no longer does. Furthermore, what seems to have caused the problem is a different program.
The culprit was a program named CallCenter (companion to the Android app of the same name). I terminated it and CTRL+D came back to life. Checking its options dialog revealed that a CTRL+D hotkey had been set up. I promptly disabled this.
Looks like this has potentially been a false alarm, but please do quickly check to see if you can replicate the problem at your end.