The generation of groovydocs performed by "grails doc" will result in duplicates for each class. If you have a class doctest.DocTest the groovydoc will be generated for this class and for a non-existent default package (see attached example application). This is more of a groovydoc bug, but I think this issue might serve as a hint for those facing the same problem.
A possible workaround:
In the _GrailsDocs.groovy script line 114 change the sourcepath from "." to "grails-app". This skips the "src" directory though, which is not an acceptable solution.