Boy, This is really frustrating... I ran all the measurements again, and ran a new configuration. The optimized results looked pretty much identical to the first set of optimized results. I compared the filter channel response curves with what I imported into MiniDSP, and the peq curves that generated. Using the export feature from MSO, along with the import feature from MiniDSP, my HSU information and SVS information seemed to have gotten swapped somehow, as the curves did not correspond correctly. I then manually copied and pasted the biquad information, and got the curves to all line up and be looking the same, minus the attenuation mentioned. Here's what I ended up with:
This is a measurement of all 3 subs, at the main listening position, before running MSO
This is the same measurement, post optimization, with biquad info having been input into the MiniDSP plugin using the import feature
This is the same measurement, post optimization, having manually cut and paste each biquad into the corresponding PEQ slot (bq 1 into peq1, etc.)
@andy_c I did rename the sub channels. One thing I found very interesting was that when I entered all the information in the config view (adding channel, filters, associated measurements) I entered them in this order SVS(sub ch1), HSU(sub ch2), Ultimax(sub ch3). After the optimization finished, the SVS and the HSU had flip flop Ed on the tree. That's what clued me in to taking a look at the biquad values displayed in MSO to see how they translated into MiniDSP- they didn't go in as they should have.