I fixed it! (for me at least)
I found that the problem is with the gradle plugin.
When i changed
dependencies {
classpath 'com.android.tools.build:gradle:1.4.0-beta6'
}
to
dependencies {
classpath 'com.android.tools.build:gradle:1.3.1'
}
in my build.gradle project, it fixed the problem.
Like the OP, I was able to sign assemblies created using the IDE's play button, but not only the ones I created using the option "Create signed APK ...".
After searching, I discovered this open problem .
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