private downloads unable to view uploaded files in dir

This is driving me insane. It seems to have started after the 6.14 Drupal update.

there is a fictional directory system/files that redirects to somewhere outside of the main site when your download method is set to private. OK, so anything I upload through drupal, such as user profile pictures, file field or image fields etc.. they all go there, and I can type in system/files/image.jpg to see it. Works. But if I upload anything via FTP for instance, like an image, to the same exact directory as image.jpg.. I type in system/files/image2.jpg but it redirects me to 404 page not found! I dont understand, looking at the directories through FTP, they are in the exact same place, have the exact same permissions, everything... So, I have no idea whats going on or why this started, only that it was working before.