Sometimes the email client will manipulate the appearance of the email because it is quoted content, or appeared in a previous email.
I know for example, that Gmail will actually hide the content of a previous mail to show you only new content.
In the screen shot, my boss' signature is trimmed because it is not the first message from him in the thread.
Think about it this way, sometimes a browser will "paint" a link in a different color to indicate that it has already been visited (purple for the popular ones). There might be a similar mechanism in the mail client. If for example, you send the same email twice, the second one might appear different as it's content has already been viewed previously.
I assume that the formatting issue is something that is happening on the users email client. There is not much you can do about that other than explicitly defining colors and styles for each message that is sent.