Why are my custom email messages sent without styling?
I FINALLY found the solution to this problem, commerce kickstart is theming the emails using the mail.css provided for the mime mail module, this file is located in the Omega Kickstart theme that was the one Im using, for some reason my custom messages were not styled using that file, so I did some of research and found this post where they explain how to theme mime mail emails, and they reffer to an issue about using different admin theme than your default theme so they suggest add the mail.css file to all your themes folders...

Well so what I did was to make a subtheme of the commerce kickstart admin theme and the omeka kickstart theme, then I placed the mail.css file in the css/ folder of both, now my custom messages sent with message notify from rules are sent with the correct styling!!

Thank you!