Miamiman,
The text for the emails is specified in the language file for JFBConnect. You can find this in /language/xx_YY/xx_YY.com_jfbconnect.ini
The language strings change a little for 4.0, but not for 4.0.1 (not sure what you upgraded from). If you can check that file and look for the following strings, that will help determine the problem:
COM_JFBCONNECT_NEW_COMMENT_SUBJECT="New Facebook Comment"
COM_JFBCONNECT_NEW_COMMENT_BODY="This is an automated message from JFBConnect.\n\nA new Facebook comment was posted by %s\n%s\n\nYou can administer the comment at that page or at developers.facebook.com/tools/comments\n-- JFBConnect"
If they aren't there, add (and translate them). If they are, let us know, as that's obviously not correct.
Thanks,
Alex