It seems there's a threshold where FOP does not align page number references correctly when generating tables of contents in PDF documents. I see that you have a reference to this in your FAQ (question 3.10), but it says "The most recent FOP releases should have this problem fixed", I'm seeing this problem with 0.94. (I have a sample FO document I will attach, looks like the initial bug reporting interface doesn't let me do this.)
Created attachment 21060 [details] FO file that demonstrates the problem
Created attachment 21061 [details] DocBook source that was used to generate the FO file (Just in case anyone needs this. It was run through the DocBook-XSL-1.73.2 stylesheets.)
Created attachment 21062 [details] Resultant PDF output from FO sample previously attached
resetting P2 open bugs to P3 pending further review