The problem is that they're 6x9's....the oval design is conducive to distorting, especially when you push them to their limits. Your HU wasn't providing quite enough to power to make the distortion incredibly noticeable, but when you made the jump to 40 watts, that distortion becomes much louder and much worse. You should set an HPF on the speakers at around 80 or so, set your gains properly, and dont turn up the bass on your HU settings. That's about all you can do...but there's only so much you can do with 6x9's
"The world is full of people who want nothing short of perfect,
but settle for less, blinded by their quest for purpose."