I have had experience with SuperContainer before in FileMaker 11/12, but not since.
Any problem I ever encountered with SuperContainer was that either all users could have access, or none could.
As your issue seems very plugin specific, I think your best bet is to call/post your question to 360Works' support site.
Depending on your setup, this solution may not even be using the plugin, but check a possible java block;
On that users machine, point a browser to URL yourServerIP/SuperContainer/ then try to upload using a default button and set permission details when asked.
All users accounts on this windows 7 client system can successfully open the documents except 1. That account when I click on the container nothing happens. When I put the URL directly into any web browser the documents opens with no problem.