Just a note that may require some history books...
I believe the FIRST set of Ultegra STI 9-speed shifters were double only. I am pretty sure on this as I only remember 3 click-positions on the left shifter... Not 4 like they are today.
If the bike is 100% new I woulda thought they woulda not charged you the $45 at all... But even so $45 is not a bad amount of green-backs...