Unable to get doxygen reference output with Boost documentation

When i try to build Boost documentation for my VMD library I receive, at 
the end of the output:

"xslt-xsltproc.windows ..\bin.v2\doc\msvc-11.0\debug\vmd.docbook
file:///C:/Utilities/Docbook/xml/dbpoolx.mod:7254: validity error : 
Redefinition of element code
<!ELEMENT code %ho; (%cptr.char.mix;)*>
                                        ^
validity warning : Attribute id of element code: already defined
  %common.attrib;
                 ^
	lang		CDATA		#IMPLIED
	^
validity warning : Attribute last-revision of element code: already defined
  %code.role.attrib;
                    ^
role		CDATA		#IMPLIED
^
warning: cannot find macro `BOOST_VMD_IS_EMPTY'
warning: cannot find macro `BOOST_VMD_IS_BEGIN_PARENS'
warning: cannot find macro `BOOST_VMD_REMOVE_PARENS'
warning: cannot find macro `BOOST_VMD_ASSERT_IS_ARRAY'
warning: cannot find macro `BOOST_VMD_ASSERT_IS_LIST'
warning: cannot find macro `BOOST_VMD_ASSERT_IS_SEQ'
warning: cannot find macro `BOOST_VMD_ASSERT_IS_TUPLE'"

I am using Quickbook to write the documentation. All previous output up 
until the errors above was OK with doxygen finding my header files.

The final documentation is produced but the reference section built from 
doxygen comments in my header files is completely blank.

If I use doxygen directly on my header files, using the exact same 
parameters in the doxygen section of my jamfile.v2 for the 
documentation, the final doxygen output does contain the information.

I am using the latest tools from the Boost trunk.

Any ideas why I cannot produce a doxygen reference section ?