Ok we think we have a fix for the problem.
From the current release of the module the method UploadForm on FileDataObjectManager does not have a hidden field to specify the DataObjects owner, e.g. the PageID.
We have commented out line 365 in FileDataObjectManager in method EditUploadedForm which does a loadDataFrom($dataObject) call. The hidden field is correctly added to this form (PageID) but the loadDataFrom method call overwrites the value in the Field as $dataObject, which is the record created from the UploadForm request (which didn't contain the PageID field).
Maybe it is that we haven't followed the documentation correctly, but the absense of the hidden field from the UploadForm suggests that something there has been over looked.
Will there we any effects from our change that will break other functionality?