I don’t know the direct answer to your question of the top of my head, but what I would recommend is to switch over to the coldbox.cfc programmatic config. You’ll probably be hard-pressed to find many people who use the XML config and it’s going away entirely in 3.5.
Of course, if you’re not using the XML config, then this might be a different issue entirely and a stack trace would be in order. (Also, make sure you restart your CF instance after an upgrade to clear out any cached CFC instances in application.)
Oh, I guess I do have an answer to your question about an upgrade guide from 3.0 to 3.1:
http://wiki.coldbox.org/wiki/WhatsNew:3.1.0.cfm
Thanks!
~Brad