Not linking correct urls for member content

Currently I am not able to get my members to the correct URL to download a pdf. When I am logged in as admin (www.mysite/wp-content/uploads/2013/09/filename, it works correctly, though when logged in as a member, it tried to link to http://www.mysite/2013/09/filename, thus they cannot access the file.
Originally I had tried to protect the downloads using the masked URL but couldn't get it to function properly. Have since deleted the masking categories and access limitations. Should I re-install or something?