I installed the latest nightly build, cleared my cookies and BOOM. I lose all my styles, and can't log into admin because it keeps trying to point to /wp-login instead of /blog/wp-login where my installation is. I was able to restore my old installation by downloading the build from Jan 2.
My blog is installed in a sub dir off the root. In order to verify (or see if I'm nuts) I would recommend trying a fresh install of the latest nightly build in a sub dir off the root, clear cookies and see what breaks.
I even tried doing a fresh installation and that broke as well, see the result here: