Sorry if this ends up being a user question, but I thought there's a chance there's something wrong with either khelpcenter or Skrooge's docbook.
I've compiled and installed Skrooge from git here into my $KDEDIR with all my other KDE modules. However, when I launch KHelpCenter I'm unable to find Skrooge's documentation, be it in the "Application Manuals" or in alphabetical list in the glossary. However, if I try to open Skrooge's handbook via Skrooge itself, it works fine.