I had some trouble with that when I switched from Redhat to Debian. What finally helped me was to (as root of course) do a "#chown -R yourusername.yourusername evolution/" and then start evolution. I had figured that the uid would be the same, but of course it's not in different distros, and maybe in different occurrences of the same distro, depending on what order you add users.
Hope that helps, it made all my filters and mailboxes etc. come right back. You could also import your mailboxes from the Evolution menus, and then set up your accounts anew. I seem to remember having a few oddities upgrading from 1.2 to 1.4, like they said you had to re-create ... something. Look around for info on that, I'll do a little looking too.