NS> OK, here's one.  Do you still have the old project file handy?  If
NS> so, can you check the lines that contain the above variables and
NS> verify that they look like this:
NS> 
NS>  '(<var> <value> t)
NS>                  ^
NS>                  |
NS> The presence of `t' here is what tells JDE to put the value into
NS> the customized-value property upon load.  If it is missing, then
NS> that's your reason why the new project file doesn't contain those
NS> variables.

Great advice, Nick.  Thank you!  Indeed this prj.el file has been
carried along for several jde revs and many of my customized variables
(all customized using the recommended emacs interface) were not marked.
This problem is now fixed.

Thanks again!
-- 
Robert

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