Well if you're rooted and messing around with ROMs or just system settings in general, check to make sure you haven't messed anything up, or that the ROM you're using doesn't have any bugs with sound. My phone shares ROMs with it's international variant, which is almost exactly the same, but it has different sound drivers and a HSPA+ radio. Anyways, the different sound drivers means that if the ROM isn't pre modified, then you can get a really tinny audio effect.
If you use a CM based ROM, check your DSPmanager. You may have something messed up in your headphone's tab
finally, it may just be because of your location. If you're out and about, or if you just have any background noise, then it'll slightly muffle and mess up your sound quality. With a computer you're at home without the same amount of background noise. Your car speakers are obviously larger than your headphones, they'll be much less affected by random noises in the background.
just a few thoughts.