Are you 100% sure you are uploading to the correct directory? The web uploader literally is a surrogate for the FTP, and dumps files in the exact same directory. If files are working via web, the only possible error is that you are not uploading the files to the correct directory.
It has to be ss_media/new
Another less likely possibility is somehow your web-host has something misconfigured where when something is uploaded via FTP it has the wrong permissions which is not permitting Symbiostock to process the file, but that is very unlikely.
An easy way to test is upload something via the web and make sure that you see it in the directory when you FTP as well.