Well, Autodesk still has the "Autodesk Sabotage" - er, I mean the "Autodesk Shared" directory. Whenever you install something from any version, it might overwrite things in here, which is the root cause of a lot of these issues.
They've been getting somewhat better with this over the years, but as long as they still have a single "Autodesk Shared" directory that is shared between all releases of Autocad, there will probably continue to be some measure of issues. They don't seem to be as bad as they used to be, but there's still weird "quirks".
Because of past experience, I actually have not yet tried installing the 2009 beta on a production machine - I'm using it in a VM. But if it's like 2008, there will probably be a few "quirks", but hopefully nothing major.