I am having a similar issue with my 06 900. I put a hypercharger on with stock pipes. I ran it that way for 6 months and my mileage was down the same as yours. About a month ago I put on a PC III and the closest map has not changed my mileage on the last two tanks. I called a few places today and they told me mapping the PCIII for my set up won't change the mileage much. The best thing I could do is put on exhaust to help the out flow of increased air from the hypercharger. Sounded good to me but who knows....maybe they are just trying to get more of my money.

Sooo maybe you need a new intake to put more air in the system.

 

I had an '07 900 Custom that had a K&N Intake system, cobra pipes and a cobra fuel commander. I got 52mpg's with it. Not sure what to do - I know I appreciate your sharing your experience with me as it lets me know I am Not going nuts!

 

Most shops that tune the Power Commanders for the big twins use external oxygen sensors in both exhausts, and then use a PC and the USB to tune the Power Commander to the bike. If you are lucky you will find a map that fits, but unless you are configured exactly as specified for the map you are using it is not at all accurate.

Another issue with some K&N filters, and with all oiled fabric containing cotton or natural fibers. If you ride in the rain or very high humidity, the natural fibers get hydrated from the water and decrease air flow. That confuses the Power Commander fuel map, and results in burning more fuel.