Whatever caused this bug seems to be gone in 7.5.
Is there any known way to update/replace Xorg from 7.4 to 7.5 for TC 2.x ?
UPDATE:
This bug appears not to be exclusive to the Alt key, but more generally to wm key bindings.
e.g.: I have added '<Key key="F12">root:1</Key>' to ~/.jwmrc-keys, in order to get the
root menu with a single keystroke. Whenever Alt+X key bindings would cease to function,
same happens to F12.