Hm, that's odd.
This can happen on models with a limited number of DSP blocks, when the keyboard runs of DSP to supply multiple MIDI song channels and panel parts at the same time.
But Genos has 28 DSP, so it's unlikely that in this case you're running out of DSP. You can check this by using the mixer. Move to the Song page / effect tab, and watch the DSP assignment for the song part that holds the organ while the MIDI is playing back.
Did you record using MIDI quick recording? Or record in stages, adding new parts one at a time?