I have just installed W3-Total Cache on my website waterwaywatch.org which is running the Atahualpa Theme on WP 3.01.
I installed manually via FTP and I was watching the transfer of files when suddenly the wp-content/plugins/ folder vanished!
Naturally, as a result all plugins have been 'deactivated' (I have printed out a list so I can easily install them all again) and I currently have no apparent no obvious way to log-in to the site.
I am not blaming W3-Total-Cache but as it occurred during installation I am report this event so it can be investigated.
There was another curious event that happened earlier this morning which might offer clues of an entirely different cause - instead of a single daily backup of content, I received dozens which were sent simultaneously - does this suggest an earlier breakdown of the built-in WP cache?