I'm afraid the information you were given is accurate. Your EBCI boarding number was based on when it was purchased when they first rolled it out Sept 2009. Now everything at Southwest is revenue-based. It stinks for some of us.
But imagine just where your spot in line would have been without it?
FYI same thing happened to us Sept 2010 - chatting with folks around us because we were surprised to get such a high number when we purchased within minutes of the date opening. I actually wrote to Southwest but did not receive an explanation. I learned the cold hard facts here.