If the User Setting "Copy Internet User Preferences" is selected, the user preferences are copied from the server to the workstation when the user signs into any workgroup. When the user quits or restarts, the preferences are copied back to the server. However, if the user is logged into At Ease under a Finder workgroup, the Internet preferences are not copied back to the server.
The workaround is to switch to a Panels or Restricted Finder workgroup, with the At Ease menu, before quitting or restarting. The internet preferences will then be copied back to the server.
This issue will be addressed in a future release of At Ease. There is no known time frame for future At Ease releases.