Matt, if the problems you are hearing are a function of your room treatments, the first reflection panels are the most likely culprit. It is very easy to overdampen the midrange and high frequency sound in a listening room. Most rooms use a combination of diffusion and absorption in order to effectively deal with first reflections without sucking the life out of the music.
If you find that the sound gets better as you remove the first reflection panels, you might experiment with diffusion as an alternative to the absorptive panels that were removed.
If you find that the sound gets better as you remove the first reflection panels, you might experiment with diffusion as an alternative to the absorptive panels that were removed.