I can not explain that behaviour, but I know that it is correct or at least known.
In the installation path of Publisher is the Publish Annotiation Table localised (C:\Programme\Autodesk\Inventor Publisher 2011 R1\Help\Autodesk_Inventor_Publisher_PublishAnnotation_Table.mht). Therein is among other things this behaviour listed.
Due to the limitations in DWF and ADR we can only publish annotations when the current snapshot option is selected. Since the annotations in DWF are global we cannot really map the annotations from Publisher when publishing the entire document. Hope that answers your questions.