Sounds to me like midi notes getting hung up as rove suggested. I have gotten stuck with a few faulty midi interfaces... Not specifically with the minibrute, but on different synths, and have encountered the same kind of problem and in my experience it was some kind of cable or interface that was not keeping up with note on/off messages properly, resulting in infinitely sustained notes, as if you were to just hold down some random key, while continuing to try and play the rest of the keyboard.
Of course it could still be a problem with your minibrute, but do you have some other way to test and maybe narrow it down?
Can you bypass all your midi interface hookup, just plug minibrute into computer via USB, and use its midi interface directly, and see if you still run into the same problem?