I think I missed a burried CGI file that needs permissions changed (I'm not sure). My site reverted to old templates without being told to. This screws up the entire site layout.
Also, I switched from markdown with smartypants to rich text and it keeps changing it back to markdown with smartypants. It's also not saving any changes I made regarding trackbacks.
Reported on Movable Type 5

Hi Chelle,
It won't surely revert to old templates itself, unless somebody is telling movable type to do so.
Have you cloned a blog and changed the templates on the cloned one? Only that way it could be that an entry or something rebuilt the blog that still has the old templates.
As for the files permissions, you should simply have the .cgi files from inside the CGIPath folder (not also sub-folders) set to 755.
Kind Regards,
Mihai Bocsaru
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