Hmmm, Specifically, lots of animes have a flaw on Audio System.
I have some original Dvds of Naruto and Bleach, and they have Dolby Digital 5.1. Watching it on a good built Home Theater (you need build one, not buy one) is really awesome.
Maybe your animes have bad audoi quality(are they original? do they support your Sound System, surround, 5.1, 7.1, 3.1,4.1?) or maybe sound system isn´t good enough