Have you tried compiling with the log file verbosity set to ‘Diagnostic’ (the highest level)? That might tease out more information. Tools->Options, Projects and Solutions, Build and Run, and then set “MSBuild project build output verbosity” to “Diagnostic”
If that fails, I think the source for the tool that is generating this message is in the NETMF source tree. One could run it in the debugger and/or add additional log statements to get it to output exactly what it is upset about.