Blog Templates deleting plugin settings from Default Template

So today I came back to a project that is using New Blog Templates that should copy pages and plugin settings (all set via the NBT plugin settings page) to any new blog created.

It used to work fine, about two weeks ago when I was last working on the project.

Today, when creating a new blog, using the single blog template I have set up, the various settings (held in custom tables and selected properly in the NBT settings) for the blog being used as a tempalte, are being deleted and therefore not copying across to the new blog.

Pages seem to be copying fine, but my custom plugin tables are getting wiped. This seems to be a recent issue.

Anyone else experiencing this and is there a fix?