>   We are running Enterprise and have purchased CFMX7. The installer
> actually refused to 'upgrade' an Enterprise Jrun installation.

The documentation and the release notes show that unfortunately there
is no upgrade path (at least no easy, built-in upgrade path) for CFMX
6.1 on JRun 4 ("JRun config") to CFMX 7 on JRun 4 ("multiserver
config").
http://livedocs.macromedia.com/coldfusion/7/htmldocs/wwhelp/wwhimpl/js/html/wwhelp.htm?href=00000027.htm

 
>   I'm now trying to figure out how to upgrade the 'virtual' CFMX
> servers, or more specificly how to upgrade each virtual server in turn,
> but keep all the settings.

See the suggestiong about the cf6settings directory in 
http://livedocs.macromedia.com/coldfusion/7/htmldocs/wwhelp/wwhimpl/js/html/wwhelp.htm?href=00000027.htm



>   I'm not a CF person. I'm just the Unix admin who makes the
> infrastructure run.
>   ColdFusion server is probably the most complex (and has the most
> layers) of any bit of software we run!.

You've obviously never touched IBM WebSphere ;-)

-- 
Steven Erat
http://www.talkingtree.com/blog/
--

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