Gradle Version: 3.0
Operating System and JVM version: Windows 10 64 Bit, 1.8.0_60 64 bit
AFAIK, Gradle guarantees that the compilation classpath will have a consistent (while arbitrary in regards to transitive dependencies) order.
It seems that starting with Gradle version 3.0, the order of the classpath entries of an Android project isn’t consistent anymore. This is a problem when using the Kotlin plugin because it breaks incremental compilation. I summarized the problem in https://code.google.com/p/android/issues/detail?id=221007.
Basicly, depending on whether you launch the build from Android Studio or from JRebel for Android, the compilation classpath will have two entries swapped.
When I reverted to Gradle 2.14.1, the problem seemingly disappeared.