We've hit this a couple of times now and I have a small fo showing the
problem.

In production we are using fop-1.0, but I've generated this on both
1.0 and 1.1rc1 (with a small patch from Vincent related to 
http://apache-fop.1065347.n5.nabble.com/page-number-is-stuttering-tt36312.html
page-number-stutters  )

See the top of the second page of the generated pdf: the text is indented ~
5 chars and missing the word "appears".

The full sentence is shown below.
                <fo:inline margin-left="4pt" font-weight="normal">
                  While most PNFs remain benign, between 10-15% become
malignant. Deep-seated PNFs are at particular risk for development
                  <inline xmlns="http://www.w3.org/1999/XSL/Format";
font-weight="bold">MPNST</inline>
                  .  MicroRNA misregulation appears to be a critical event
in the malignant transformation of PNFs.
                </fo:inline>

I apologise for the funky fonts, but this problem is so delicate
w.r.t. content that I cannot switch out my fonts at this time. 

The juxtaposition of the two simple-page-masters is critcal.  The
gap/loss always appears on the "three-side" page layouts. I have
removed any overflows (Vincent ;) ) so I don't thing that as the problem.

http://apache-fop.1065347.n5.nabble.com/file/n36563/short.xml short.xml 




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