Android ZipAlign does not run on generate signed apk

Question

Does anyone have experience with zipalign not running even when explicitly set when building for the store? I am running Android Studio 2.0 beta 2 from canary channel.

signingConfigs {
    release {
        keyAlias 'key'
        keyPassword ''
        storeFile file('location.keystore')
        storePassword ''
    }
}

buildTypes {
    debug {
        debuggable true
        zipAlignEnabled true
    }

    release {
        debuggable false
        zipAlignEnabled true
        signingConfig signingConfigs.release
    }
}

If I build with generate signed apk it won't do zipalign even though it says in my build logs that it does. If I push app to phone and build that way it will sign and do zipalign. The other method of course can be fixed by using zipalign -c -v 4 unaligned.apk aligned.apk so was just wondering if there was something I was missing with generated signed apk.