Can we get a link to your site?
In all the other upgrades I’ve done, I can’t reproduce this issue. Yes, I understand the *outcome* you’re experiencing.
I’m looking at it from a *code* perspective.
On a working-as-expected upgraded site running 3.0 with the network enabled, trying to access the /files/ folder directly will always result in a 404. But the images will show.
(need a link? I can give you several.)
So, testing that part specifically won’t help.
Sometimes even though mod_rewrite is enabled and permalinks aren’t working, images fail to show because in fact the htaccess file is being ignored.
Please check and make sure Apache is forced to read it. ?? Ask your webhost if you can’t get in there, or add
AllowOverride FileInfo Options
to the vhost entry for that web account.
99% of the time, this has fixed the issue.