I know this is obvious so please dont take offense, but are you SURE that all of your phase relationships are correct between all the drivers? Its easy to assume you did everything right but overlook something simple.
Im also a "pro" and I struggled with the MS-8 until I went back to basics with my system and worked out all the phase relationships taking into account the various crossovers in my system, I ended up reversing the polarity of my underseats because of an amp crossover messing things up (RTA showed a dip as well) and then used to the "Kaigoss workaround" for the sub calibration. Now everything sounds great.....basically once I found "the method" for my setup I was able to get consistent, good sounding results.....but getting there was definitely a challenge.
Kaigoss also has a good point about efficiency.....the MS-8 doesnt put out a ton of power....it works great with the relatively efficient L7 speakers, but maybe not so good with your Focals.