Mailing the story:
NetworkManager: Ubuntu 8.04 to 8.10 upgrade breaks it
Yep, I used wireless to upgrade from Ubuntu 8.04 to 8.10 and finally 9.04, and NetworkManager lost control of my wired Ethernet interface in the transition from 8.04 to 8.10. I did manage to find a fix very quickly, and I can confirm that it does indeed work.