I just installed this and running on test site for now.

I'm using this discount link:
$this->add_cat_to_cat(4, 5, "%", 50);
Buy 1 item in category 4 and get 50% off an item in category 5.

Seems to work good, apart from:

One of my items in category 4 has a master category of 9 and is linked to category 4.

If I browse to that item via 'category 4' I get the discount message.

No discounts are applied if I add the item and an item from category 5 to my cart and the discount message does not appear if I browse to the item via 'category 9'

Is there any way to stop the discount message from appearing when viewing these linked products?