I've recently added a MiniDSP 2x4 box to my system and am experiencing the same drop of signal level. For instance, I had to increase the volume on my AVR from -22dB (without DSP) to -12dB (with DSP) to achieve the almost equivalent levels shown in the below measurements.
View attachment 47732
I've got the 2x4 jumpered for RevA (0.9Vrms) and am receiving the signal from my Marantz SR7002 AVR. The BASH 500s subwoofer plate amp has sufficient gain headroom to compensate for the drop, but I am also dealing with an amplifier induced thump on transition to standby. The higher the gain knob on the amp, the louder the thump. So adding the MiniDSP to my system has now made my auto-sensing amp so annoying that I am switching it on and off regularly like a pro amp.
Like the OP, any suggestions as to improper use of MiniDSP or is the the nature of this device?