Inconsistent fade envelopes

Kinda similar issue here. I’m trying to loop a multi instrument using a destination marker and a transition marker. The audio pop as the transition cursor hit the destination fade-in, as if it let the transient pass through. Here’s an example:

https://youtu.be/qFAtmXJeCX8

Could it be related to this framerate issue and is it possible to eliminate this poping effect without affecting the performances too much ?