I tried upgrading from ColdFusion MX 6.0 to ColdFusion MX 6.1 on my Linux based web server, and all hell broke loose. So rather than choose to upgrade, I gutted CFMX 6.0 and did a brand new install, and things are back in order (sort of).
CFMX 6.1 is a heck of a lot faster than 6.0, which pleases me of course, although now that I did a fresh install, there are broken bits all over the place that will take me an hour or two to reconstitute.