Window Mangers :: 4.1RC1 - JWM - Ctrl+D - keyboard shortcut
The keyboard mapping of Ctrl-D in JWM overrides the mappings for the 'dfm' file manager, and also blocks using Ctrl-D to exit from Python.
First, issues related to release candidates belong in release candidate threads. There are often many changes between release candidates and the current release candidate is 4.2rc1 -- 4.1 is out of rc status. If you're not interested in testing, you should upgrade to 4.1 release (which is presently also marked as current in the mirrors).
Second, that's the problem with setting bindings -- the window manager hogs whatever bindings are set up and prevents anything else from using them. The bindings are changed from C to CA and SC in 4.2rc1. Ctrl-d operates dfm rather than jwm in that version.
You should edit your keybindings according to your personal needs and preferences. Not everyone uses python, not everyone needs ctrl-d available. It's all a personal preference.