This happens every time I do a deploy. For instance if my folders are numbered up to pathToThumbnails/0000/59 on my local machine and I have since uploaded new images via Attachment_fu on my server and the folders are numbered up to pathToThumbnails/0000/125 on the server, when I deploy the folders are now back down to pathToThumbnails/0000/59 on the server and my app can't load any of the images.
Using MiniMagick.
I think it might be gremlins.