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.

If the file you are uploading via the web does not show up in the /public_html/ss_media/new/ directory, yet Symbiostock is processing that media, then the only conclusion is that for some reason when you log in via ftp you are navigating to the wrong directory.

Go to the Symbiostock forums and PM me your login information as well as FTP information and I'll check it out for you.