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What do you mean by soft synth track? A simple instrument track, the MIDI track of a MIDI/audio pair or the audio output track of a MIDI/audio pair?
Are you perhaps putting a MIDI FX on an audio track or an audio FX on a MIDI track?
Do the notes actually disappear from the grid, or are they just skipped during playback? If skipping is the problem, double the buffer size in "MIDI buffers, prepare using xx ms buffer".
Otherwise, a little more info is necessary.
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