I just got this problem last night, too. Sooloos firmware 2.394 but iPad still on iOS5. After a reboot of the MD600 it was all fine again. I'm not really liking software updates that don't fix any important bugs but do add new "features".

Rowland Model6/BPS6, Rowland Coherence II, Levinson 390S and 37, AudioAanZee Reference Flow music server, Rowland Aeris DAC, Rowland Cadence phono stage, Pass Labs Xono phono stage, Yamaha PX-2 and Thorens TD 160MKII, Transparent Ultra and Reference cables, Apogee Diva magnetostatics (refurbished).