I saw the following post on another MS forum that while not related to the question above may shed some light on the issue:
On Windows 64bit Windows Media Center is a 64-bit executable. If you build your assembly (DLL) as an x86-based assembly only the Windows Media Center on an x86 machine will open it.
This has to do with the nature of .NET applications more than anything else. The value of the AnyCPU option is that an assembly built with that option can run on any .NET platform unmodified. Once you pick a platform for the assembly that assembly can only run on the targeted platform.
The short answer is, unfortunately, you cannot register a 32-bit assembly to run as a plugin on 64-bit WMC
Perhaps the issue is that you need to provide 32 bit and 64bit CE?