I agree, it is unusual, but the same thing happened to me in 2007. I was audited for 2003 and 2004, the result of the audit was: I overpayed in both years and was issued a refund for $1800 and some change. I though woo hoo, I get some of my change back.
Low and behold, 2 weeks later I received notice that my 2005 and 2006 tax years were going to be audited. Net result: I owed the IRS the entire balance of what they had just refunded me plus $4.00 as they disallowed some of my deductions (a total crock of crap, imo). It turned out to be a wash.
I’d bet that if you hadn’t owed anything or been due a refund after the first audit, the second audit never would have taken place. They just didn’t want to have to send you that $1800, so they played loose with the rules, and cleared away the refund. Slimy bunch of turds.
Role playing: Advisor to agent, "You know, Mr. Smith, that my client would appreciate your continuing with this audit through 2010 and 2011. He pays me good money and we have trucked over 1000's of pages of support and we have interrupted our calendars to accommodate you here today. As you can see, he has nothing to hide, so we deserve an expedited review. Please take your time and let us know if there are additional materials which may need to complete your work."