Do you have the center speaker in an entertainment unit basically enclosing the center speaker. That would give you the muffled sound. With a restricted space like that, you cant use a bigger center channel and you are going to face the same issue with other small center speakers as well. Even if you had more apace, it is not a good idea to enclose a center speaker or any box speaker, if that is what you are doing.
For $400 you could get better used center speakers than those tiny ones. Unfortunately you don't have the space.