Thanks for the info. The reason I explicitly asked for the message is because I too have not been able to do an auto-upgrade for a couple of weeks now and I see the exact same message you reported.
So I ran a very simple test:
1. On one of my blogs where I don't use Suffusion, I deleted the installation of the theme completely (it was present, but not active).
2. That installation of WP had very few other themes and none of them had any updates available.
3. So I uploaded an old version of another theme designed by another person (the theme I uploaded was version 0.7.0 of Hybrid) on to this blog.
4. After uploading Hybrid, I see the same message. Hybrid has a new version available (0.7.1), but auto-upgrade seems unavailable.
5. I checked on another blog of mine where there was no installation of Suffusion at all, i.e. there was no Suffusion folder there to start with. I see the same message.
What is interesting is that on localhost I actually am able to do an auto-upgrade for everything.
Then I ran a Google search for the message "automatic upgrade unavailable for this theme". One of the very first hits that came up was this:
http://wordpress.org/support/topic/354240?replies=4. Looks like a lot of people started facing issues after upgrading to 2.9.1. Another link that was very interesting was this:
http://code.google.com/p/kaytwo/issues/detail?id=911, with posts dated 14th January.
My first thought was that somehow the notification that Suffusion provides about a new version being available is messing things up. But then I have had this notification since
version 3.1.9, released on 19th January, while people have been facing issues since
5 days before I did anything in the theme to affect this behavior!
All in all, this is a hairy mess. Luckily, it is calming to learn that Suffusion wasn't the architect of this failure.