If your email client supports HTML encoded emails, I would expect the content to render using the HTML version of the message being sent out from your instance. However, in order to better understand this issue I would recommend submitting a case in your secret customer group here in the Jive Community so that the next available support engineer can perform an investigation specific to your instance. When you submit the case, if you could include the following, it should assist:
1. A copy of the email you receive in your email inbox, including full headers ( FAQ: Configuring and Troubleshooting Email Integration )
2. Is this behavior occurring for all message templates once they are customized?
3. Are you seeing the same behavior for default/OOTB message templates?