I've got a plugin I've been working on. A coworker installed nextgen gallery .98 and suddenly my shortcodes started misbehaving. I've disabled the nextgen plugin and luckily for this site its not needed. Thought you should know though.
What it does is starts adding html encoded quotes around all my shortcode values. Completely breaks it of course and I don't really think I should have to look to strip them out. I think I read somewhere that WP itself used to have this similiar problem. Something to do with all shortcodes needing to be processed before the_content gets sanitized.