Many people have complained time and time again about the .NET Obfuscator that comes with Visual Studio (2003 and 2005) not working effectively with CF applications. I too have had my applications running and working until I obfuscate it using the tool that comes with VS and then my app doesn't behave correctly...
Well.... believe it or not but there are loads of .NET obfuscator tools available out there, I admit not free, but you get what you pay for in life ;)
Once you have obfuscated your code, you can use a free tool such as Reflector to check the results.
See this link: http://www.howtoselectguides.com/dotnet/obfuscators/