it was a bit boomy in mine also, but that's how the original IR sounded too.

was that last preset using the Mesa MKII? if so, the amp's controls only really control the tone that goes before the distortion....kinda like a variable pickup eq. the good/bad thing is that they also added in a scooped eq after the amp that you can't change. it's a little too scooped, hence the boomy bass and shrill highs. nothing an eq can't fix though.