This has now been resolve, please ensure all windows updates are applied.
Click here – If you require assistance with RemoteApps
“We have found out that it is a known issue and our internal team is working on it.
EVENT_SYSTEM_FOREGROUND comes too soon on the server. We end up sending the incorrect z-order to the client because in some scenarios the z-order calculation has not completed before we send it. A race condition exists in RemoteApp when a window is activated resulting in the activated window opening behind the previous foreground window. After the RemoteApp widow is activated, RdpShell.exe checks the server z-order before win32k.sys finishes computing the new z-order. When this condition occurs, Rdpshell.exe sends the wrong z-order instructions to mstsc.exe on the client. This fix introduces timer code to cause RdpShell.exe to wait for win32k.sys to finish computing the z-order before sending the new z-order to the client.
The fix is likely to get released by March or April.
I will provide you with the update, as and when if there is any.”
“I’ve been informed by Microsoft Support that the the hotfix currently is scheduled for release at March 21st.”