Resource files not outputted

I have an annotation processor that produces both some java source files and an xml file.
When the compilation fails, though, only the contents of the generated java files is shown and the xml file seems to be ignored, even though it should effectively have been generated.

The xml file is outputted in the SOURCE_OUTPUT location and uses the standard Filer methods.

The generatesFileNamed() method to does report the file to be present.