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I thought those of you following this thread may like to see how it turned out. While I have yet to get an official confirmation from MACR on the issue, I did post to the Flex forums and in general the engineers there are very good at getting back to folks.
On both machines I can now safely use the WS as long as I a) add an alias to jrun-web.xml and b) use the alias when I call my WS.
While I'd still like to know more about why this error occurs (especially since host/foo.cfc is ok but host/foo.cfc?WSDL is not), at least now I have a consistent URL and my Flex app (can I say - I love Flex) is running ok.