No-one has noticed this bug so far. Maybe only my Fossapup has it, but maybe not. I wrote about it in this post.
On Fossapup64-9.5, JWM 2.4.0 and 2.4.3:
when all the windows on the active desktop are minimized (not with the "show desktop" button), the JWM keyboard shortcuts stop working.
(Vanilla dpup 9.3 is not affected probably because it uses Xwayland.)
JWM sets the input focus to None while it should set it to the root window. According to the Xlib manual,
If focus is None, all keyboard events are discarded until a new focus window is set…
Workaround: I've made a patch for JWM 2.4.3 that seems to work. It's just a snippet copied to clientlist.c from main.c where it's used for initialization. I don't know how to do it better.
Thanks to @Eastler_Dart for helping to reproduce the bug.
Edit: It's related to conky, see viewtopic.php?p=87851#p87851 below.