I think you mean fsck, not fsk. That is a normal file system check and is expected on the first reboot after an OS update. So is trackerd and hildon-thumbnailerd, reindexing your media database. Let them run to completion, it should be OK after that.

Your folders will look empty while fsck is running because the file system is unmounted. That is normal.

As for the rotation lock, there is a setting for it in System -> Settings, if I remember correctly. Sorry, my N900 runs Thumb but is heavily modified and cannot be used as a reliable reference.