I believe there might be a bug in the Domain Mapping plugin as it relates to Jetpack.
After I connect a new subsite to the domain mapping plugin, I get the error message below when attempting to connect that same site to WordPress.com in order to use the Jetpack plugin. I then have to go to Network Deactivate Jetpack and then reactivate it:
"Invalid request, please go back and try again.
Error Code: invalid_request
Error Message: The URL stored by the Jetpack servers does not match your site. Please try disabling the Jetpack plugin, re-enable it, then connect again."