Go to the Mag+ Settings panel in the plugin. Click on the triangle next to "Device templates".
Click on the icon under "T" for the iPad Retina and make sure that it is linked to the correct template [Applications > Mag+ > Mag+ templates > Apple iPad Retina]
If this does not solve your problem you can choose to use Export Rule "Centre" as it doesn't really matter as the ratio is the same for both devices.
Let me know how it works out!