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Source: Microsoft Support
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On a computer running a 64-bit version of Microsoft Windows, you use the Microsoft .NET Framework 2.0 Configuration tool to configure the .NET Framework security policy.
The changes made using the .NET Framework 2.0 Configuration tool do not apply to a 64-bit .NET Framework 2.0 application. 64-bit .NET Framework applications are assemblies compiled in Visual Studio with the Target CPU set to "Any CPU" (and running on a 64-bit computer), x64 or Itanium.
The Microsoft .NET Framework 2.0 Configuration tool only applies to 32-bit assemblies (i.e. assemblies compiled with the Target CPU set to x86). This is also true for the mscorcfg.msc MMC snap-in located in the \Program Files\Microsoft.NET\SDK\v2.0 64 bit\bin folder.
This behavior is by design.
Run Caspol.exe for the 64-bit version of the .NET Framework 2.0 to configure security policy for 64-bit applications.
1. Open a 64-bit .NET framework SDK command prompt or the Visual Studio x64 Command prompt. 2. Run caspol.exe to make the policy changes.
You can verify changes to the security policies saving them out to a text file and comparing. To save the policies to a text file, run the following command using both the 32-bit and 64-bit versions of Caspol.exe
Caspol –all –l > c:\policy.txt
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