Yeah, yesterday I was using the arpeggiator and it somehow shut off the midi out's right in the middle of recording the line! The guy I was working with was screaming, and me just frustrated as fuck. After 2 minutes of trying to solve it I simply restarted Cubase and it was perfect! (BTW, that's the #1 studio tip you can ever tell someone: just turn it off. Kid you not, from ProTools to especially analog equip and mixers; with analog it has something to do with sending that burst through the lines)
Another syncing quirk: don't even bother trying to run Cubase and Rebirth simultaneously if you're tweaking lines and use the audio side of Cubase. The midi stays good, though.