Duplicate elements appearing in emails that the plugin should not be handling

hello

Ive just bought your email customiser – and it mostly works great. But one email is having problems. I send emails for “partially shipped” items. Ive stopped your plugin from sending that email – keeping it with the usual one that we send. But with your plugin enabled, it duplicates the tracking information in the email! That is even with your plugin not handling that particular email.

Do you know why? It is specifically the part of the email that shows the tracking info. I would add an image but I cant do that here.