No room correction done, the signal goes from a CD-player/transport digitally to a DAC and then balanced via analog signals to the pre-amp and then to two monoblocks. No DSP's or other stuff involved. They're not even close to muddy.
My room is quite treated though and perform quite well, and the dimensions are calculated according to Sepmeyer's golden ratios (it's built solely for hifi/movies from the ground up). They are perfectly balanced, I've measured them too and they are quite flat as far as I can see (of course my room isn't 100% perfect so it will affect the result in some way). Some of the drivers are changed from the old F1.1F but it still sounds weird that the old model wasn't performing well. Are you sure the room acoustics and electronics were good enough?
Your measurements must reflect room reflections, my measurements doesn't look like that at all. Can you set the "measurement time" in the software? You have to look at the first 10 ms or so to get the correct response from the speakers, after that all room contributions mess up the curve.