As others have mentioned, it's very likely the MiniDSP was being overdriven at the input. I have a bunch of them, being used in cars, small active home speaker systems, and until about 6 months ago, my HT. I've only experienced an issue with the HT subs, and during loud bass passages the sub drivers would often make a "click" type of sound...similar to a driver bottoming out, but not exactly. Right around last Christmas, I replaced the MiniDSPs in the HT with a BiAmp TesiraServer, and haven't experienced the same noise. Granted, this isn't a very scientific approach to troubleshooting said noise, but it did lead me to believe the MiniDSP was the culprit. With that said, I have no qualms with MiniDSP products. They're a fantastic cost/feature/functionality product, when used correctly.
Also, bumping any EQ to +12 is asking for trouble. The true, proper way to use an EQ is to cut only, but of course, we all use them to bump things into line, anyway. If adding gain with an EQ, it should really be limited to +3, maybe +6 in extreme situations. Anything beyond that is demanding a ridiculous amount of more power from the amplifier at those frequencies, and is likely to add distortion and heat in both the driver, and amplifier. Huge dips in response are usually room related, if the driver and enclosure are chosen and built correctly. The real fix to those issues is placement in the room, as difficult as that may be in most people's homes. For example, if I moved my seating position 2' forward, I'd be in bass heaven, but my room is small, and moving the couch is not an option for me. Trial and error with placing the subs helped, and adding additional subs to fill the dip also helped, a lot.