did you install memcached or apc plugin? If you did, remove them and try it. Probably its caching problem.
Update: I am not sure if this is your case but i was facing this problem when i try to use apc for opcode caching. Basically main problem is fcgi prosesses are not using same cache pool. Here is more details: https://bugs.php.net/bug.php?id=57825 What can i suggest: dont use opcode cache or use memcached for opcode caching.