I have to confess, I have a -bunch- of other stuff loaded - I only listed the extensions that seemed most likely to be relevant....
I just tried the same thing after booting base norestore and loading -only-
Xlibs Xprogs Xvesa wbar jwm emelfm2 minefield7 and filezilla (and their deps)
and I -am- experiencing the problem as described.
Note that I am on a different physical box than earlier, though booting from the same media, and I am having a hard time getting Xorg to run so using Xvesa instead.
I suspect it is the Xvesa vs. Xorg-7.5 difference that is allowing me to see the issue.
I -have- made changes to my .jwmrc* files, which changes would not be present with "base norestore", however I don't remember any such changes that would be relevant.
More testing as time permits.