I have not. I'm no expert and I can't be sure for your case, because Art's work is totally dependent on your system configuration (how many subs, placement, how capable are the speakers, and so many others) and subject of a high degree of variables. Because of that I remember Art generated a lot of support request/patches/etc. when released and I'm sure they can't have solved any possible scenario (it's impossible).
However your description make me think you should reduce the support requested to some speakers/subs or change how low some speakers are allowed to go, because they are asked too much (demanding more bass hits more heavily on speakers than other frequencies and can easily brings distortion).
Are you using passive speakers or passive subs?
Do you experience the same distortions at lower volumes?
I guess if you put the subwoofers closer to you they should also gain more headroom, but as everything it's a trade-off and may not work if they became to easy to localize.
P.s. I advise against having one room correction on top of the other, there are already soo many variables