"Cannot determine expansion folder" when running android Instrumentation tests

We want to set up instrumentation tests for our app, that also has 2 flavors. We have successfully set up Android Studio to run instrumented tests directly from the IDE, but trying to run instrumented tests from the command line via 'gradle connectedCheck' always results in the following error:

FAILURE: Build failed with an exception.

* What went wrong:
Execution failed for task ':app:mergeDevelopmentDebugAndroidTestJavaResources'.
> Cannot determine expansion folder for /Users/james/Development/AndroidProjects/parkinsons11/app/build/intermediates/packagedJarsJavaResources/androidTest/development/debug/junit-4.12.jar936209038/LICENSE-junit.txt with folders 

Our test app, which also has two flavours and is set up for instrumented tests, runs both from the IDE and from command line without incident.

Here is our gradle file from our main project:

buildscript {
    repositories {
        maven { url 'http://ift.tt/1dRjIBX' }
    }

    dependencies {
        classpath 'com.crashlytics.tools.gradle:crashlytics-gradle:1.+'
    }
}
apply plugin: 'com.android.application'
apply plugin: 'crashlytics'

repositories {
    maven { url 'http://ift.tt/1dRjIBX' }
}

android {
    compileSdkVersion rootProject.ext.compileSdkVersion
    buildToolsVersion rootProject.ext.buildToolsVersion
    defaultConfig {
        applicationId "com.app.ourapp"
        minSdkVersion 16
        versionCode 11
        versionName "1.1"
    }

    buildTypes {
        release {
            minifyEnabled false
            proguardFiles getDefaultProguardFile('proguard-android.txt'), 'proguard-rules.pro'
        }
    }
    sourceSets {
        main {
            assets.srcDirs = ['src/main/assets',
                              'src/main/assets/font']
        }
    }
    compileOptions {
        sourceCompatibility JavaVersion.VERSION_1_7
        targetCompatibility JavaVersion.VERSION_1_7
    }

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

    productFlavors {
        live {
            versionName "1.1 live"
            applicationId "com.app.ourapp.live"
        }
        development {
            versionName '1.1 development'
            applicationId "com.app.ourapp.development"
        }
    }
}

dependencies {
    compile fileTree(include: ['*.jar'], dir: 'libs')
    compile project(':library:datetimepicker')
    compile project(':library:tools')
    compile 'com.android.support:appcompat-v7:+'
    compile 'com.android.support:support-v4:+'
    compile 'com.crashlytics.android:crashlytics:1.+'
    compile 'org.quanqi:mpandroidchart:1.7.+'
    compile 'commons-io:commons-io:2.+'
    compile 'joda-time:joda-time:2.+'
    compile 'com.microsoft.azure.android:azure-storage-android:0.4.+'

    testCompile 'junit:junit:4.12'
    testCompile "org.robolectric:robolectric:${robolectricVersion}"
    testCompile "org.mockito:mockito-core:1.+"

    androidTestCompile 'junit:junit:4.12'
    androidTestCompile "org.mockito:mockito-core:1.+"
}

And here is our gradle.build from our test app (which works):

apply plugin: 'com.android.application'

android {
    compileSdkVersion 22
    buildToolsVersion "22.0.1"
    defaultConfig {
        applicationId "com.test.picroft.instrumentationtestapp"
        minSdkVersion 16
        targetSdkVersion 22
        versionCode 1
        versionName "1.0"
    }
    buildTypes {
        release {
            minifyEnabled false
            proguardFiles getDefaultProguardFile('proguard-android.txt'), 'proguard-rules.pro'
        }
    }
    productFlavors {
        newFlavour {
            applicationId "com.test.picroft.instrumentationtestapp.newflavor"
        }

        oldFlavour {
            applicationId "com.test.picroft.instrumentationtestapp.oldflavor"
        }
    }
}

dependencies {
    compile fileTree(dir: 'libs', include: ['*.jar'])
    compile 'com.android.support:appcompat-v7:22.2.1'

    testCompile 'junit:junit:4.12'
    testCompile "org.mockito:mockito-core:1.+"

    androidTestCompile 'junit:junit:4.12'
    androidTestCompile "org.mockito:mockito-core:1.+"
}

I'm at a loss as to where I'm going wrong. I've compared the directory structure from both apps and there's no meaningful difference. Here's a rough outline of our main project's structure:

src
-androidTest
--java
---*
-live
--res
---layout
---values
-main
--java
---*
-test
--java
---*

I'm totally confused why instrumented tests on one app works fine both in IDE and in command line, while the other refuses to work via command line.