Published applications from XenDesktop/XenApp are launched before the WEM agent ends processing settings.
This is causing some settings configured from WEM to be used by the published applications are not getting applied before the applications are launched as it is required.
In the Studio console, go to the Applications node and open the application Properties and go to the "Location" page.
In the "Path to the executable file" field put this path "C:\Program Files (x86)\Norskale\Norskale Agent Host\VUEMAppCmd.exe" which is required when using WEM with published apps from XenApp/XenDesktop.
In the "Command line argument" field put the path to the actual published application executable, for example for Notepad "C:\Windows\system32\notepad.exe".
Note: You can also edit the WEM policy configured to tell the WEM agents who is the WEM server and enable the setting "VUEMAppCmd extra sync delay" and then under the "Extra launch delay" option enter 1000 or 2000 ms to add 1 or 2 seconds respectively to ensure that the necessary agent work is completed before the app launches. Then run the "gpupdate /force" command on the agent machines from where the apps are being launched to apply the policy change to them.
To use the Workspace Environment Management agent with XenApp and XenDesktop, it is required to point the published applications to VUEMAppCmd.exe (located in the agent installation directory) with the application path as a command line argument.
Refer to article https://docs.citrix.com/en-us/workspace-environment-management/current-release/user-interface-description/actions/applications.html (see the "Tip" section).