Don't worry - fixed it myself. For those who want to know, there is the following tag set in the default manifest file. By default, this is set to:
android:theme="Theme.Black.NoTitleBar"
Changing it to the following fixed it:
android:theme="Theme.DeviceDefault"
Quite simple I guess :).
Update
As of org.apache.cordova.dialog v2.9.0, the guys on the Cordova project changed the Android source to contain a default theme value to a hard coded value, as follows:
new AlertDialog.Builder(cordova.getActivity(), AlertDialog.THEME_DEVICE_DEFAULT_LIGHT);
It is frustrating, but you can comment out this line and replace it with:
new AlertDialog.Builder(cordova.getActivity());
To restore previous behaviour and have Cordova use the value specified in AndroidManifest.xml.