Permalinks not working correctly in RC3 build

Ok, this has been happening with all the development versions so far. I switch permalinks to /%postname%/, all is well until I edit a page, change the content and update. When i go back to the site 80% of the links take you to the wrong page. This was happening with posts too but i think that has been fixed. Anyone have a solution for this? I know they are saying this is the last candidate before final release, but this seems like a pretty big issue. Any one else having this problem.

p.s.
It happens after a clean install too.