It takes the computer a few miles to 'learn' about any changes that are made to the air/fuel mixture. If they did a stock run on the dyno, changed the intake while still sitting there, then did another dyno run, the car didn't have time to relearn the mixture, so it would have been at something other than the most efficient for the equipment installed. That's my guess anyway.
One thing I will caution you about. Changing the intake is OK (you can always swap back to original), but having a tune done to the computer puts your 5 year/100k mile powertrain warranty in serious jeopardy. Also, JMO, but $1250 for a 40RWHP gain seems a bit much.