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This issue has been resolved in NWP 2.0.3 released today.

Thanks Hamid, that's exactly right: Nisus Writer Pro 2.0.3 resolves this issue, where TOC, index, and cross-reference page numbers could be incorrect when making a printout/PDF for certain documents.

As far as I can tell, all of my documents with this problem seem to be formatting properly now. Thank you very much. That's a big relief.

However, when I open some documents saved using 2.0.2 which used to exhibit the problem, I get the message "There were some problems while reading this document." After I rebuild the TOC using 2.0.3, the message does not appear again. Just a note to those who might have seen this problem in the past, it might not hurt to rebuild the TOC.

kstephens wrote:As far as I can tell, all of my documents with this problem seem to be formatting properly now. Thank you very much. That's a big relief.

Excellent, I'm glad to hear it!

However, when I open some documents saved using 2.0.2 which used to exhibit the problem, I get the message "There were some problems while reading this document." After I rebuild the TOC using 2.0.3, the message does not appear again. Just a note to those who might have seen this problem in the past, it might not hurt to rebuild the TOC.

You should be able to safely ignore this warning, though certainly rebuilding the TOC would clear out any stale/incorrect TOC associations that might be lingering.