For those that are interested, we figured out the root of the problem and the fix. Maybe this will help someone down the road. Thanks to all that responded.
As it seems all the domains/accounts hosted on our VPS are top level; so we couldn’t use robots.txt to fix this.
The problem:
-We have a handful of websites using a shared IP address – Only sites with SSL cert get a dedicated IP
-Some of these websites have additional A record DNS names (mail.domain1, ns5.domain2, etc) that all resolve to that shared IP address
-Within your browser if you went to one of those records it would pull up the website (account) that is first alphabetically within that shared IP pool
-It’s assumed that a website or multiple websites somewhere in the web must have linked these domain names somewhere on their webpages – so search engines crawled them for the content of that first alphabetical website
-Search engines then indexed the content of that site for these other DNS A records and displayed the alternate URLs in the SERPS
The fix:
Edit Apache’s httpd.conf file on our VPS – adding a new (first listed) virtual directory of that shared IP address to point to the servers cpanel default cgi page instead of listing one of our hosted accounts first.
This page describes what we needed done and what fixed it for us: http://forums.spry.com/cpanel-whm/1568-how-can-i-change-default-page-ip-address-points.html
Thanks again!