I don't know if I should start a separate thread, but I have a similar problem.
Within the admin area, I receive the little orange notifications that plugins need to be updated. But when I go to either the new Dashboard>Update area or the Plugins screen, there aren't any plugins requiring updates.
I compared the versions of my plugins against another blog where notifications work fine. I can then identify which plugins are out-of-date and manually update them via FTP.
But why would the admin area not indicate which plugins need to be updated when some portion of WordPress knows enough to give me the little orange update indicator?
This problem only appeared after updating to WordPress 3.0 and I have other blogs with 3.0 that don't have this problem.
Anyone have any idea what could be causing this?