Check the Apache error log - I wonder if you might have the same “symlink protection” interfering here similar to what was happening in another thread.
Also it helps to enable rewrite logging when you have any rewrites and suspect that they are getting triggered (for example if file/dir is immediately deleted or not created, you’d be hitting the framework handler).
http://httpd.apache.org/docs/2.4/mod/mod_rewrite.html#logging