Reason: Some times, CitrixCseEngine.exe takes longtime to process GPOs. In that case the published desktop application will respond even after logoff check time of application launch. But published application was unable to respond after logoff check time.
As I said in previous article you can increase time delay value as temporary fix.
Root cause: RDP session also takes long time to login. One of the root cause was Active directory replication. My situation, users are in one domain and XenApp servers are in another domain. Replication was broken and CitrixCseEngine.exe was taking long time to process GPOs.
Solution: Force replication or wait for full automatic replication between two domains.
Please use above solution as is based on your decision.
Have a nice time!
