Whether sending an email from Salesforce using the Send an Email button in Activity History (Standard Match My Email) or in the Visualforce component Email Messages (MultiMatch Match My Email), if you use an email template it is important to be aware of the differences between text and HTML. Text versions of email allow for searchable text, but does not allow for formatting and the inclusion of colors and logos. HTML version does allow for formatting of graphics, but is not searchable.
Salesforce has been designed to send email out as both a text and HTML version. Thus, in providing a feature to send email from its custom object (for MultiMatch users), the same protocol is followed. Based on the knowledge base article within Salesforce, it is recommended that email templates are created as HTML and the plain text part is left empty. In this manner, when an email is sent, Salesforce will automatically create the text version from the HTML code.
This was brought to our attention at Match My Email because our app was matching email accurately, but the body of the email was the unmodified plain text from the template. Users were clicking Send Email, selecting a template which was a text template, and modifying the text. However, the changes were made to the HTML version, not the text version. Once sent, Match My Email was matching and uploading the plain text version of the template which was unmodified. Email clients typically have a preference to display HTML version, and so by using only HTML templates, emails going out will still follow the Salesforce protocol of being sent as both HTML and plain text, but both will contain the same modified text.