On a XenApp 5 farm on Windows 2008 server, all published applications launch slowly and do not launch in seamless mode (The application would be presented in a fixed size window). The issue affected both streamed to server applications and normal applications such as a simple published Notepad.

The issue started after several Microsoft hotfixes had been deployed using Windows update. The procedure in CTX102750 - Seamless Applications Launch in a Fixed Window did not resolve the issue and there were no permission related problems. Recreating the ICA listener also did not fix the issue.
However, published desktops and non-seamless applications (fixed size resolution or percentage of screen) launch quickly.

To resolve this issue, configure mfaphook.dll in the AppInit_DLLs.

Note: The path in the preceding image is for x86 system. In a 64 bit OS, you need to define mfaphook.dll and also mfaphook64.dll as both are used. They have different paths as "progra~1" is for Program files and "progra~2" is used for Program files (x86). For a x64 system, the dll on the path must be mfaphook64.dll. For x64 computers, check for the mfaphook.dll at:
HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Microsoft\Windows NT\CurrentVersion\Windows\ AppInit_DLLs

Adding the dll avoids failures in scenarios where the short names in the 8.3 naming convention cannot be resolved at the server. Refer to CTX131995 - User Cannot Launch Application in Seamless Mode in a Provisioning Services Server when XenApp Optimization Best Practices are Applied.

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Problem Cause

This error might occur if Citrix Hooks are not being loaded. From a process monitor log, it was possible to see that mfaphook.dll was not being loaded.

From the export of the registry key HKEY_LOCAL_MACHINE\Software\Microsoft\Windows NT\CurrentVersion\Windows\, it was possible to see that the value of AppInit_DLLs was blank and did not contain the mfaphook.dll.

This article provides resolution when the seamless applications start slowly and launch in a fixed size window.

CTX107824 - Citrix API Hooks (mfaphook.dll) Explained and Enumerated

CTX131995 - User Cannot Launch Application in Seamless Mode in a Provisioning Services Server when XenApp Optimization Best Practices are Applied