If the minidsp sounded phenomenal (I assume you mean transparent), as expected, then it means Dirac is messing up room/speaker eq.I did that (went to a minidsp with Dirac from marantz with audyssey) and are now going back because in my case the AVR room correction was far superior than the minidsp.
The minidsp without room correction sounds phenomenal though, but my room is garbage.
Unless you find your Marantz receiver more convenient in your system, if I were you I would go back to the minidsp (if you still own it) and tweak Dirac parameters. There is no reason you could not get a very similar eq compared to what Audissey does.
I would first look into limiting Dirac processing to low frequencies (say <500 Hz) and listen/measure again.