Problems creating a TOC for a book.

This message, annoying thought it can be, only means that FM's diligent validation gnomes have spotted that your book includes .fm files with different definitions for Dark Grey. If you're not doing anything advanced like using Colour Views, you could simply copy the colour definitions (File > Import > Format) from the first file before the one that triggers error to that suspect file and all the files that come after it.

On the other hand, I don't remember having this sort of mild discrepancy actually block generation of a ToC. Have you tried with all the .fm open?