Thank you everyone for your replies!
Here's my findings so far:
Rather than disabling Q-Necron's rays, I created a new module with four different types of beholders on the map.
Then, I created an 18th level sorcerer, buffed him, and strolled up to the first beholder, cast an AoE spell on the Tyrant and just let the PC take a beating, while watching for antimagic cones. When the first beholder died from the AoE spell, I went to the next one and just stood there, whilst being pummeled by eye rays.
I did this over and over again.
In all of the two hours I tested, I saw ONE (1) antimagic cone and it was on the beholder NOT equipped with the cone. This beholder was not attacked by an AoE spell either.
All of this on a standard module with no custom material at all.
I just don't get it.
Thanks!