I just spent a couple of hours setting up a multisite system, installing and tweaking many WPMU DEV Premium plugins and other plugins.
Then I started creating sub-sites, and none of them worked. There were messages like, "Error establishing database connection," and messages about the database needing to be repaired.
So I tried uninstalling plugins, one-by-one, to identify the culprit. Apparently the damage was done, because the problem persisted even after all plugins were removed. So I started from scratch, adding plugins and re-tracing my steps (adding and checking subsites after every step) to see where the problem started.
After you install the AVH FDAS component of the Comment Spam Pack, the WPMU DEV Update Notification plugin announces that a new version is available, with the option to update automatically. This update is what destroys the subsites. After checking version numbers I realized that the update notification is linking to the standard (non-WPMU-DEV version) in the WordPress repository, which is version 3.0.5. The problem is apparently that the WPMU DEV version is set up one way, but the mainstream version is not.
Is there any way to turn off erroneous update notifications like this? I'm afraid of something like this happening with other plugins, and I don't want to lose any more hours of work...or, worse yet, to have something like this happen when the site is live with clients. I'd rather keep using the Updates Notification plugin, but I want to eliminate this risk.
Sorry for the long message.