X-refs are not working in the PDF output

I correctly generated a PDF from a ditamap using DITA-FMx and cross-references are not working.
Thanks for your help.

Thanks Scott, although I don't think this is the best solution in our case.
The target PDF is a file that is delivered to a customer. This means that it won't keep the same location on the file system, and therefore links will no longer work I guess. In addition to that, we are still not ready for publishing our doc on the web. So the delivered PDF is a file that lives on its own.
If the problem occurs only across different nested ditamaps, I thought I could get rid of these nested diatamaps and just have a global ditamap containing only topics. But then how would I obtain the different section levels in the TOC?
Today, I use nested diatamaps in order to get the following structure:
|_ Section 1
|
|_ Section 2
|_ Section 2.a
|_ Section 2.b
|_ Section 2.c
|
|_ Section 3
where Section 2 is a ditamap with three topics.
Are there other alternatives to nested ditamaps in order to keep the same level of indentation?
Thanks
Arianna

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X-refs are not working in the PDF output

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