I dont know if this will help you - but I use a Tascam US 144 USB audio card/unit. Every time I boot up Cubase with a virus project, I need to change the latency setting on the TASCAM from NORMAL, to low, or vice versa, to get the midi and arps to play back in sync. Just one of the irritating quirks to deal with I have found.. if you have a similar option with the E-MU card, try doing that and see if it helps?
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