I noticed that intermittently seamless XenApp 6.5 published applications would stay on top of other windows even when they were not active. In my case I been utilizing the Citrix Receiver Enterprise 13.1.0.89 to take advantage of the Pre-Launch feature.
Was able to replicate the issue with all Receiver versions 3.x, even with the new 3.4 client which also works with the Pre-Launch feature of XenApp 6.5
I did not experience the same problem with legacy clients 11.2 and 12.1 (Don’t use these clients with XenApp 6.5)
Environment
- Windows 2008 R2
- XenApp 6.5
- UPM 4.1
- vSphere 4.0 <- What the heck? I know, I know

- Citrix Receiver 3.x
Cause:
The issue exact cause is unknown, but seems to be related to changes in the gain focus behavior of the new Citrix Receiver 3.x. I contacted Citrix support on this one, and after they thought I was crazy, I was able to replicate the problem while on the phone.
It seems that a Seamless Application Window does not become the active window if you make a local window active while the seamless connection initiates.
Resolution:
After speaking to a senior Citrix support specialist, he directed me to an old Citrix article. Applying the Registry key changes mentioned solves the issue (TWISeamlessFlag = 1)
For x86 systems:
1. Edit the registry:
HKEY_LOCAL_MACHINE\Software\Citrix\ICA Client\Engine\Configuration\Advanced\Modules\WFClient
2. Create a string value, REG_SZ, called TWISeamlessFlag with a value data of 1.
For x64 Systems:
1. Edit the registry:
HKEY_LOCAL_MACHINE\Software\ Wow6432Node\Citrix\ICA Client\Engine\Configuration\Advanced\Modules\WFClient
2. Create a string value, REG_SZ, called TWISeamlessFlag with a value data of 1.







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