Classpath order is not deterministic with Gradle 3.1 RC1

Git repo:
It’s an android project that uses kotlin and dagger.
I’ve added classpath printing to kotlin and java tasks (in doFirst).
Running ‘assembleDebug’ multiple times, I’ve noticed that classpath order is often different (which forces Kotlin compilation).

Gradle Version: 3.1 RC1
Operating System and JVM version: Ubuntu 14.04 64 bit; JDK 1.8.0_102

The issue does not seem reproducible for me with Gradle 2.14.1 and Gradle 3.0.

Sounds similar to:

Could there be something else (a configuration change with the switch to 3.1 RC1) that could have caused the new behaviour? It seems the issue (or a similar issue) exists for longer already and it might be a problem with the Android plugin: