I have just installed a fresh copy of 3.6 on my localhost. If I change the Permalinks to something other than Default, each link clicked display a 404 error. This was not like this yesterday when I was using 3.5 locally.
So I am wondering if it related to 3.6? I did not see it mentioned in the 3.6 Master List.
FYI, no plugins installed and using 2013 theme.