I use the machinedrum and cubase at the same time, then again, i dont do any sequencing with cubase itself.... The workaround that I have found works quite well with my MC-909 and my machinedrum is setting them up as remote machines. Therefore they are all trigerred by a midi message coming from cubase, but use their own clocks to sync.
I make techno and drum n bass, so timing is definatly important, and i've found the using them as remote machines does a pretty good job.
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