I tried this on the .org forums, but no responses... such a hit or miss over there.
I attempted to run the automatic upgrade to 3.0.1 on both of my WP sites, but the upgrade stopped at the "downloading update" stage and wouldn't continue. I tried the Memory Bump plugin, but that did not fix the problem. I should also mention that on this server I have probably 5 or 6 WP installs... some of them upgrade, and some don't.
IF the auto upgrade is not working then you will need to do the manual method of downloading the latest version and overwrite the existing. Remember to backup first before doing that. Also, backup your wp-config and the database.
That is what I do when it can't upgrade automatically.