The validator in the tooling relies on output from the build. More generally, this is true of other aspects of the tooling. For this reason, you'll get best results by leaving auto-build enabled.
That said, in the latest version of the tools, the validation is now invoked during the configure goal, which should mitigate false errors like this (since the configure goal is executed in process-classes, which means the source should be compiled).
Hope that helps explain things a bit.