I used the tool midi-ox with the midiyoke dirver and found out the the problem is with my software sequencer. In the recording mode it skips the first note irrespective of the tempo set. When SD1 sends "start" message, the sequenceer sends a bunch of sysex messages, and as soon as SD1 sends the first "clock" message, the sequencer sends the second note. The sequencer should have prepared to send notes as soon as it received "start", instead it is preparing after receiving the first "clock" message. So it has no time to send the first note synchronized with the clock signal already received.

-Dimu