Hello Maru,
I've rendered this on Rebusfarm with approximately 120 machines.
They've done the setup, and therefore I do not know their configuration, but I guess, trust and also hope, their machines are all equal.
I would suggest talking to them (if you are in contact) about their setup. Perhaps one of them is reading this right at this moment...;-)
What I can tell, is that there are small sequences in the CMasking_ID channel that share the same colours, so I guess they were rendered on the same dedicated machine. And the problem has its origin at render distribution and render start across multiple machines. The random ID assignment should perhaps be fixed with an identical seed in the scene, but this could be difficult with moving objects that are not visible at the start of the animation.
My machine is 3dsmax 2015 with corona 1.3 and a few of the latest Sigershaders.
The scene has copyrighted material in it so I would rather not like to put it here on the forum, but I can send it to you if you send me your contact info.
best regards,
Ceasare