Citrix | Popup: You already have an instance of this application opened and are not allowed to run more than one instance.

When an user received the following popup message in his screen (note this is a picture from the event log)

Application popup: Connection Error: You already have an instance of this application opened and are not allowed to run more than one instance. Please contact your System Administrator.

Well it sounds easy you logon as administrator to the Citrix Servers and look if the users is disconnect. Unfortunately in my case it wasn’t that easy. After looking on 2 Citrix servers I found out that the user wasn’t logged in at all. So I checked the following things first before looking further.

1. Look for remaining user profiles in the user folders on both of the Citrix servers.
2. I looked for the profileguid in the registry

Again no clue why??
At the end it happened to be a Windows update probably which was installed earlier (only not on a few days before.)
How I figured this out by checking to logon with the Remote Desktop Connection (RDP) to one of the Citrix servers. This way I could exclude windows issue or any other issue. Logon via RDP was possible with the user so it was related to Citrix.
I re-applied the 2^nd rollup for Xenapp 6.0 and did this on both of the servers. After rebooting first one server and disabling the other server I could see if I could logon. This was possible, next was the other server and after the reboot the issue was gone.