If I use the outline extension to generate PDF bookmarks it generates a 
complete set of bookmarks for each page-sequence I have.  In other words, if I 
have this input:

<?xml version="1.0" encoding="UTF-8" ?>
<fo:root xmlns:fo="http://www.w3.org/1999/XSL/Format">
	<fo:layout-master-set>
		<fo:simple-page-master master-name="simple" page-
height="29.7cm" page-width="21cm" margin-top="1cm" margin-bottom="2cm"
			margin-left="2.5cm" margin-right="2.5cm">
			<fo:region-body margin-top="3cm" />
			<fo:region-before extent="3cm" />
			<fo:region-after extent="1.5cm" />
		</fo:simple-page-master>
	</fo:layout-master-set>
	<fox:bookmarks xmlns:fox="http://xml.apache.org/fop/extensions">
		<fox:outline internal-destination="sec1">
			<fox:label>Section 1</fox:label>
		</fox:outline>
		<fox:outline internal-destination="sec2">
			<fox:label>Section 2</fox:label>
		</fox:outline>
	</fox:bookmarks>
	<fo:page-sequence master-reference="simple">
		<fo:flow flow-name="xsl-region-body" font-size="10pt" font-
family="Helvetica">
			<fo:block id="sec1">Section 1</fo:block>
		</fo:flow>
	</fo:page-sequence>
	<fo:page-sequence master-reference="simple">
		<fo:flow flow-name="xsl-region-body" font-size="10pt" font-
family="Helvetica">
			<fo:block id="sec2">Section 2</fo:block>
		</fo:flow>
	</fo:page-sequence>
</fo:root>

I expect to get one set of bookmarks with items of Section 1 and Section 2 
linking to the first page and second page respectively.  Instead I get two 
complete sets, i.e., items Section 1, Section 2, Section 1 and Section 2.  The 
bookmarks link to the right places.  This only seems to happen if there are 
outline references to more than one page-sequence.