How do modules end up in the profiles directory in distributions?
I found the problem.

I have two make files - drupal-org.make.yml &amp; build-xq42_d7_sk.make.yml. I was including the following in the build-xq42_d7_sk.make.yml:

includes:
  - drupal-org.make.yml


Turns out this caused the problem. There's no need to include any reference to that file at all in the build-profile-name.make.yml file.

This is the first make file I've built and I created it by reading documentation and looking at existing make files for other projects. I saw this line in one of the make files I used as an example and assumed it was OK.

Now I know...!