I have a similar experience.
I had a Pioneer Avic f900, and the JBL MS-8 revolutionized the sound I was getting in the car - it was no longer lifeless and crowded. For the first time, I had an appreciable sense of space between the instruments, proper stereo separation, and some life in the sound. And all from an iPod.
I have just upgraded to the Pioneer Avic f930, and the sound has just taken a nosedive. Significantly less spatial resolution, and a real deadening quality to everything, despite recalibrating the JBL MS-8.
I believe the problem is how the Pioneer now takes its audio