Application Personalization has been working in 10.1 but since upgrading to 10.1FR1, applications are no longer being Personalized.
Using Process Explorer from Microsoft Sysinternals tools, you may find that when looking at the dll's view the Ivanti dll EmLoader.dll is missing from the application;
Where as you should have the Ivanti dll files hooked into the application;
This can be caused by having Legacy AppInit enabled. This is enabled either via the Advanced Settings within the EM config or by setting the Engineering Registry key;
HKLM\Software\AppSense Technologies\Environment Manager
There will be a DWORD called LegacyAppInit with a value Set to 1.
To resolve the issue, you can either remove the Legacy AppInit setting or downgrade back to 10.1.336
This issue is currently under investigation.