Make sure that the feature "Rechannelize MIDI In" is set to Never (located in the MIDI menu) if you are using the Command Station as a sound module controlled by an external sequencer. If that does not solve the problem, try hitting Stop three times, or playing the Pattern by pressing Play, then Stop twice on the Command Station before pressing play on the external sequencer. Playing the Pattern will ensure that your channels load with the correct Presets, prior to being triggered by the external sequencer.