The way you describe it i think it is a well known event when sound has a sudden attack.
If you look at this image
You can see the theory behind attack-clicks.
Where the spectrum is close to the 0-dB line these will be no clicks, everywhere else there will be a click, and the further away from the 0-dB line the louder the click will be.
The solution for your Loudness automation is to initiate the change at 0-dB, and then let it raise to the wanted value in ~ 1/10 secd. That will remove the artefact-click.
OBS! You also need to have release at 0-dB! If not you will get the same click-artefact when the sound is terminated abruptly