PDFBOX-2423 is not closed yet so I'm not sure if the issues I'm having are a cause of that.
I'm using the latest trunk and I have issues with the PDPageTree.indexOf method. The javadoc reads Returns the index of the given page, or -1 if it does not exist. which I understand it means in returns -1 if the given page is not found in the page tree correct? If so, the following unit test fails:
Another similar issue I have is that PDPageTree.indexOf doesn't find the correct index for a PDPage returned by the PDOutlineItem.findDestinationPage:
Also note that indexOf is used by PDPageDestination.findPageNumber which also returns a wrong result.