Yeah I think it’s just timing. I mean, being a tenth of a second off is enough to cause an audio glitch. We cut samples to the zero crossing to avoid this, so it makes sense that not being perfectly on time when changing scenes would cause a glitch. It probably also has something to do with the gain amping up so quickly. It would be better if scenes could turn trigs on/off instead of having to use the AMP volume for tracks.
Another fix could be the option to have quantized scenes.