Good to know you got it, finally. I don't know how long you have been using REW, I have been using it for many years and would still make such mistakes once in a while though as soon as I noticed something weird I knew where to do and fixed it quickly. Believe it or not, I was going to mention the REW left/right output as a possible scenario but forgot, it was around midnight at the time.
Pogre is an experienced user, that's why he kept thinking room mode etc.. Those U shape after XO point are not unusual at all, even if Audyssey is on, it can only improve things to a point, room modes are hard to overcome no matter what auto Room EQ you used. I have tried Dirac Live, Audyssey, with and without minidsp/REW and settled on the free (not really but..) Audyssey (XT32 Sub EQ HT) as it can do a very
good job in the range from 15-250 Hz, but for people who must see a best possible looking curve (like mine and Pogre's just for example), the Editor App+REW is a must, with or without any help from minidsp. The SR5000 series are limited to the primitive XT version, but the minidsp solution could be quite effective depending on how it is used.