Hola, a mi me pasaba lo mismo y lo solucioné psando a 'audio sync' en vez de internal sync (es el botón que tiene una tarjeta de sonido dibujada en la barra de sync). Con esto se me acabaron los problemas de ese tipo. Lo vi en la ayuda donde pone:
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When SONAR is used alone, or with an external device that does not have its own clock or timing signal, you use one of two clock sources: Internal or Audio.
When the clock source is set to Internal, SONAR uses the clock built into the computer or the computer's MIDI interface as its timing source. If your projects contain only MIDI (no audio), this is the most efficient method of playback.
If your projects contain MIDI and audio, or only audio, you should set the clock source to Audio. This lets the sound card clock determine the correct speed for audio playback and automatically synchronizes MIDI playback to match the audio. For more information, see System Configuration. You cannot use the tempo ratio controls when using the audio clock, because the audio playback speed is determined by the audio clock.
When either of these clock sources is used, you can also configure SONAR to drive other MIDI devices using MIDI Synchronization. For more information, see MIDI Synchronization.
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Salud