I am trying to find the rate for 30-year Treasury securities for certain months in 2006. The IRS used to refer to the interest rate published in Fed Reserve release H.15 (average yield on 30-year Treasury Constant Maturities for the month). Now, the IRS issues a notice with the rate, based on the "monthly average of the daily determination of yield on the 30-year Treasury bond maturing in February 2036." For 2006, the rate in the IRS notice usually, but not always, matches the 30-year rate in Federal Reserve release H.15. For June 2006, for example, the rates are 5.16 and 5.15. Why is there a difference? And does this mean I should not use H.15 to look up the interest rate, even though 30-year Treasury securities are back?

For some period, the US Treasury stopped issuing (selling) 30 yr bond. During that period the H.15 did not have the 30 year rates. So the IRS came up with a method to compute a proxy rate for the 30 yr treasury bond.

The Treasury started re-issuing the 30 yr bond about two years ago so I don't know why the IRS is not taken the rates from H.15.

For pension plans you should use the rates published by the IRS.

Agreed. Use this link from the IRS site, they update it fairly timely:
http://www.irs.gov/retirement/article/0,,id=96450,00.html