Is your minidsp for the subwoofer? If so, I would just bypass the internal crossover on the receiver. However, when you talk about crossover in the receiver, there are a few. One is for your actual speakers and one is just for the subwoofer (might be called LFE crossover). The first, basically is a high pass to protect your speakers and the second is a lowpass for the subwoofer. It doesn’t appear the receiver ever changed the lowpass for the subwoofer. Both appear to be an 80hz low pass. Which is about 6db down at 80hz (where it is crossed over at). Is there any chance you might have changed the wrong crossover? Or did you change all the crossovers?
Either way, you will most likely get better results just using the minidsp and setting something like a 4th order low pass at 80-120hz and a high pass at 20hz. And then dsp down anything that is way high to get a more even response.