Ya might need to rejet/adj. air/fuel mix but what's more than likely is the change in sound is messin' with yer head.
If it wasn't for my GPS tellin' me otherwise I woulda thought the same thing - when I extended the silencer on my SBP system and quieted it down, my brain told me I was goin' slower... but in fact I had exactly the same performance as before *shrug*
Oh right, when it comes to exhaust tone, "sounds better/worse" is purely a matter of opinion lol I fer one hate
the ghetto sound of a cap-less stock pipe