WSS Agent notifier shows the update panel when the option "prompt end-user for update" is unchecked in the WSS Portal under Service > Mobility > WSS Agent > End User Permissions.
The issue has been raised to our WSS development team, and the bug will be fixed in an upcoming WSSA release. It has been confirmed there is no workaround available to resolve this problem.
A WSSA beta release would be available to the public via our Symantec Beta Program for customers that would like to get the issue resolved before the General Availability (GA) of the next WSSA release.
This knowledge-based article would be updated once it is available.
Note: The WSSA beta version will need to be pushed out to your endpoints explicitly using your preferred deployment tool.
The bug has been addressed in the latest version of the WSS Agent v6.2.1.