This is crazy. The same thing happened to me this morning. Everything was fine last night, and now, not only are my plugins deactivated, but all my pages (i.e. permanent pages) are *gone*. They still appear in the MySQL database, but wordpress does not see them.
I’m hoping there is a solution to this really soon.
CORRECTION: my permanent pages are not *gone* per se, but they appear as posts in the main blog, and not as pages. Any idea how to correct this??