I had set up a site nice and proper with an CM admin subdirectory. Added the requisite mod rewrites to make the URLs pretty. But, for some some reason, it broke all the forms in the admin subdirectory that used POST as its method. The forms would redirect to the 404 page.
The solution to this problem after much searching was to add Option +FollowSymLinks to the head of the .htaccess file. Everything worked perfectly afterwords.