This is not a new thing. I noticed it before the 2.0 firmware. In my current setup it has become a bit of a bummer.
What I find is that moving an expression pedal that's plugged into the expression inputs, will occasionally cause notes to drop out in the Arpeggiator, Sequencer and Matrix Arpeggiator. It doesn't happen all the time... sometimes it will play for a while with no issues, then suddenly drop a note, or sometimes a few notes close together. It doesn't matter if the expression pedal is routed to anything via the matrix or not. It doesn't happen when the pedal is not being moved. I've tried it with a pair of Moog Expression Pedals, as well as my old Ernie Ball Volume Pedal, with the same results. It happens on either expression pedal input.
Testing at low speeds on very simple sequences, it seems inconsistent in behavior. Sometimes it sounds like the note plays, but doesn't trigger the envelopes. Other times it sounds like the note doesn't play at all.
I don't know if it's a software or hardware issue... or maybe it's a problem with my particular machine. If anyone else has seen this behavior, it would be nice to confirm it isn't just a problem on my end.