During a recently build I added an <xref linkend="VDG-ACKS"/> (in the Acknowledgements section) and noticed this in the build log:
No "en" localization of "Acknowledgements" exists.
Don't know what gentext to create for xref to: "acknowledgements" (linkend=VDG-ACKS)
Build stdin.pdf
I suspect the lack of gentext matches for the acknowledgements section is an issue. This may explain why it was difficult to get the section to appear in the TOC as well.