Here is my test case, as simple and replicable as I could make it:
1) I compiled JWM svn 564 with "./configure --prefix=/usr; make" and installed it with the example configuration file (jwmrc) that comes in the tarball.
2) Start Xorg; test with Alt-1, Alt-2 etc. (the desktop switchers) that keyboard shortcuts work.
3) From JWM's menu start Firefox; close it with the mouse (click on the top-right "X" button).
4) Repeat step 2, to verify that the keyboard shortcuts still work.
5) Now leave Xorg and switch jwmrc from the default focus model "sloppy" to focus model "click".
6) Repeat the above steps 2-4.
The effect: with focus model "click", keyboard shortcuts work *before* closing Firefox, but no longer *afterwards*. I get this effect reliably, 100%, and also in very different setups. Here are a few observations related to the effect:
- The effect is *not* limited to Firefox (or GTK programs more generally).
- The only program on my computer that does *not* show the effect is xterm.
- It happens *only* if there are no other windows (beyond the one that will be closed).
- It does *not* happen when closing a program with Alt-F4.
- The regular Xorg shortcuts still work (Ctrl-Alt-Backspace etc.).
- Measures like mouseclicks on the desktop, opening and closing the menu, etc., do not bring the keyboard shortcuts back.
- Starting programs (e.g., Firefox again) does bring the shortcuts back.
- From memory: I recall having seen the effect already in JWM svn 562, but not in JWM 2.1.0. Have not used anything in between these versions.