I upgraded my WordPress page to 3.5 yesterday using the automatic upgrade option. It seemed to work great until I went to post something. For some reason the text editor box, and the new “Add Media” box were completely dead. It seems that many other users had very similar issues. I went through some of the same bugs and issues.
It seems as though it was related to the auto-upgrade feature and possibly rewriting permissions? I can’t be 100% certain, but I can tell you my fix was very easy. I reinstalled wordpress after the auto-upgrade by manually copying the files (EXCEPT wp-content folder and the wp-config.php file, do not replace these!!). Once I overwrote these files and uploaded the new files my site was back to 100% working order. Other users reported similar issues which included a bug within the Bulletproof Security plug-in. That bug has been patched and its recommended that you upgrade to the newer version.
Hopefully one of these fixes solves your WordPress 3.5 issues!