The fix applied for
MJAVADOC-145 causes the plugin to loose source roots that get created during the generate-sources build phase. I.e. if one runs
the plugin properly documents generated source code but running
only documents the default source root "src/main/java".
Usually, I would expect to have the JavadocReport mojo @execute phase="generate-sources" and the TestJavadocReport mojo to have @execute phase="generate-test-sources" (although it's kind of ugly to have the compile phase being run in the later case).
In lack of these annotations, the plugin produces different output when run directly from the command line or indirectly as part of build.