I have narrowed this down to aupitch using the chain in track 1.
Somehow AUPitch is messing with Renoise’s timing.
In the attachment: If you turn off AUPitch in track 1, track 2 will play fine.
Just a quick guess: Is PDC enabled in Renoise? AUPitch introduces a lot of latency.
Oh, nice! That fixed it!
In perspective with PDC on, it tremendously sounds so funny! 
Thanks Taktik!