A .ecm (minimal configuration) file cannot represent a configuration where a package has been removed from the configuration first. For example if you started with the default template and added CYGPKG_POSIX, you would get a conflict because of having two signal implementations present. This would be resolved by removing CYGPKG_LIBC_SIGNALS from the config. A configuration like that cannot be represented in a .ecm file.
This bug has moved to http://bugs.ecos.sourceware.org/show_bug.cgi?id=57324