Sorry for the delay in response. I’ve been very busy, and this issue required some research. It is more complex than it may seem.
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Here’s what I have determined:
This is a limitation in your subscription email provider (some plugin is providing this capability, JetPack is most common). The subscriber function used by the JetPack plugin, for example, does not parse WordPress shortcodes in their generated emails. This is a known limitation of JetPack and one they are actively working to fix: https://github.com/Automattic/jetpack/issues/869. The last reports indicated that the next version of JetPack (3.8) will remedy this. It appears that they will render the shortcodes in the email, thus providing the tweet this capability within the email.
Unfortunately, Tweet This can not do anything about this. This is entirely a problem with WordPress shortcode behavior and how it interacts with whatever plugin or service is providing subscriber functionality. Tweet This has no capability to do anything until after WordPress does its shortcode parsing, but if this was occurring, this wouldn’t be an issue in the first place.
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I hope I have provided helpful information, and I’m sorry I can not do more.