I have several sites that are running multiple blogs. I haven't made the switch to MU yet (waiting on 3.0 or so now).
When I use the upgrade automatically function, it works on the blogs running in the main directory (i.e. http://www.casadeblundell.com).
But if I try to run it on a blog that's in a sub-directory (i.e. http://www.casadeblundell.com/jonathan or http://www.casadeblundell.com/laurie) it seems to always error out.
Has anyone found a work around or solution?