Active applications that are NOT pinned to the taskbar will, by default, always show at the right side next to the pinned applications.
After a Workspace Refresh, the applications should still be available on the right side.
In this specific scenario where Symantec Data Loss Prevention (Blue Coat DLP) is installed, the applications will shift over to the left of the pinned applications after the Workspace Refresh is finished.
The behavior is triggered by the Symantec Data Loss Prevention product, removing the product will take away the issue.
This issue is resolved in Ivanti Workspace Control 10.2.900.0.