Android Annotations + Android Studio/Gradle builds fine, but throws ClassNotFoundException at runtime

Question

I'm struggling with moving a project from Eclipse to Android Studio and getting Android Annotations to work properly.

I've used AA in various projects without too many issues, but this has me stumped. I have the usual setup in my gradle files:

// Top-level build file where you can add configuration options common to all sub-projects/modules.

buildscript {
    repositories {
        jcenter()
    }
    dependencies {
        classpath 'com.android.tools.build:gradle:1.3.0'

        classpath 'com.neenbedankt.gradle.plugins:android-apt:1.8'
    }
}

allprojects {
    repositories {
        jcenter()
    }
}

configurations {
    all*.exclude group: 'com.android.support', module: 'support-v4'
}

and

apply plugin: 'android'
apply plugin: 'com.neenbedankt.android-apt'
def AAVersion = '3.3.2'

dependencies {
    compile fileTree(dir: 'libs', include: '*.jar')
    compile project(':libprojects:ActiveAndroid')

    apt "org.androidannotations:androidannotations:$AAVersion"
    compile "org.androidannotations:androidannotations-api:$AAVersion"

    compile 'joda-time:joda-time:2.8.2'
    compile 'com.nostra13.universalimageloader:universal-image-loader:1.9.4'
    compile 'com.actionbarsherlock:actionbarsherlock:4.4.0@aar'

    compile 'org.springframework.android:spring-android-core:1.0.1.RELEASE'
    compile 'org.springframework.android:spring-android-rest-template:1.0.1.RELEASE'
    compile 'com.fasterxml.jackson.core:jackson-databind:2.4.1.3'
}

android {
    compileSdkVersion 22
    buildToolsVersion "22.0.1"

    sourceSets {
        main {
            manifest.srcFile 'AndroidManifest.xml'
            // java.srcDirs = ['.apt_generated','src'] // We had big build issues with this left in, but it builds OK with it commented out
            resources.srcDirs = ['.apt_generated','src']
            aidl.srcDirs = ['.apt_generated','src']
            renderscript.srcDirs = ['.apt_generated','src']
            res.srcDirs = ['res']
            assets.srcDirs = ['assets']
        }

        // Move the tests to tests/java, tests/res, etc...
        instrumentTest.setRoot('tests')
    }

    packagingOptions {
        exclude 'META-INF/LICENSE.txt'
        exclude 'META-INF/license.txt'
        exclude 'META-INF/LICENSE'
        exclude 'META-INF/NOTICE.txt'
        exclude 'META-INF/notice.txt'
        exclude 'META-INF/NOTICE'
    }
}

apt {
    arguments {
        // Mark - This looks like it's not actually needed, as it builds fine without and throws up a warning when it's included.
         androidManifestFile variant.outputs[0].processResources.manifestFile
        // if you have multiple outputs (when using splits), you may want to have other index than 0
    }
}

The app seems to build OK, but I get a ClassNotFoundException immediately upon running. I've checked the build directory and no ClassName_ classes seem to be generated. Also my androidannotations.log file only has the following line:

20:11:45.159 [Daemon worker Thread 30] INFO  o.a.AndroidAnnotationProcessor:83 - Initialize AndroidAnnotations 3.3.2 with options {androidManifestFile=/Users/marky/myapp/android/build/intermediates/manifests/full/debug/AndroidManifest.xml}

Whereas another app I've build has a much longer log:

20:11:58.93 [Daemon worker] INFO  o.a.AndroidAnnotationProcessor:83 - Initialize AndroidAnnotations 3.3.2 with options {androidManifestFile=/Users/marky/anotherapp/app/build/intermediates/manifests/full/debug/AndroidManifest.xml}
20:11:58.164 [Daemon worker] INFO  o.a.AndroidAnnotationProcessor:107 - Start processing for 18 annotations on 26 elements
20:11:58.215 [Daemon worker] DEBUG o.a.h.AndroidManifestFinder:98 - AndroidManifest.xml file found with specified path: /Users/marky/anotherapp/app/build/intermediates/manifests/full/debug/AndroidManifest.xml 
...loads more lines 

So it looks like AA is not running fully, but I'm not sure why. I've searched all day on SO and other places for a solution but I can't see one.