WP 2.5 and Automatic Plugin Upgrades
By DarrylI’ve upgraded numerous plugins recently and not had an issue. However, this morning I was attempting to upgrade cforms and a few of Lester Chan’s plugins and they failed.
Unfortunately I also discovered that when the automatic plugin upgrade fails, it removes the plugin completely from the list of available plugins….and also deletes the directory. Now this obviously wouldn’t have been an issue if the plugin upgrade hadn’t failed, but since it did, it means that now I’ve got to manually download the plugin, and then ftp it to my server.
If this is going to be a major issue with automatic plugin upgrades, then I may just stop using the automatic upgrade feature altogether. Could it be that the plugins themselves are not setup properly for automatic upgrade?

I’ve had to completely stop using Automatic Plugin Upgrades on my sites/ blogs as well.
Haven’t seen what you’ve seen where the directory is deleted, but I’ve had more than enough plugins fail and generate spurios PHP errors as a result.
I think part of it has to do with the fact that in all my installations, Wordpress is installed in $DOCUMENT_ROOT/wordpress/ and not just the root (htdocs).
Symlinking $DOCUMENT_ROOT/wordpress/wp-content to $DOCUMENT_ROOT/wp-content has seemed to help a bit, but things are still very, very, buggy.
So for now, it’s back to the old tried and true method of sucking down the updates locally, and SFTP’ing them up to my host.
At least that way I always have a current backup!
I have no idea why the directories are deleted. I have each installation of WP installed in root, and with the exception of only a few plugins, they have all updated flawlessly.
I’m not sure if the error is on the plugin authors part or WP’s part.
So, like you, I am updating manually.