I just downloaded the spacedock version of this file, and the version files for the bundled Firespitter and RPM plugins are for KSP 1.0.5, not 1.1. Perhaps just add them as dependencies rather than include them? That way you don't have to update your mod each time they update. Either way, I think that is the conflict which led to the behaviour as bobvodka described. I had the same problem and I too nuked my install, then started adding back a few mods at a time to find the culprit. I can also confirm that CKAN is installing with the wrong directory structure, but the downloads (both from Spacedock and CKAN's download) have the correct file structure. Very odd.
Edit: Looks like the latest update to the CKAN file has fixed the file structure issue, but a user opting for a manual install may still have issues because of the bundled but outdated plugins.