When running MU all accounts were able to see the Footer edit page created with the theme's functions.php . Now, with WP3, only the Super Admin can see it.
I have got it working by widgetizing the footer and treating it like a sidebar as in twentyten but I would rather return to managing them as before.
The ability to do so is obviously still there as Super Admin can see it (and can see it when using Sites > Backend). If the DB had completely removed all the personalised footers I'd go for the widget option but the fact it's still there suggests there's another way.
Furthermore those who previously managed their footer through Appearance > Footer would be left with being unable to edit the text if we moved to a widget (and left the original footer code in) or if we removed the old footer code then hundreds of users would be inconvenienced by needing to put their footer in a widget.
I'm happy to PM functions.php and footer.php if it helps.