Any update on this? I can confirm that this happens to me as well on 2.2.1 with the same project structure as above.
Graeme, I cannot figure out how your solution applies to the posts above. What is this “passphrase” thing?
I do not explicitly access the project properties in my top-level gradle.build although I have a “gradle.properties” alongside it that contains common version numbers used in the dependencies section of both the top-level build file and in the sub-projects ones.
GRADLE-2837 is reported as fixed pointing at your comment but, IMHO, it is far from it.