.Net security configuration is per-CLR. This means, in 64 bit OS, there is a 32 bit .Net security configuration, and a 64 bit security configuration.

When you change .Net security configuration in 64 bit OS, make sure you understand which security configuration you are modifying.

For example, when you install 32 bit .Net framework SDK (or Visual Studio 2005, which by default, installs the 32 bit .Net framework SDK), the security configuration MMC snapin is 32 bit, and it only modifies the 32 bit security configuration.