It's really quite simple. Your discounts are based on volume across each product and not each variant. Please read below.
On settings (trays) and chains & Necklaces you receive the discount across each item rather than just one color. For instance, trays & chains are sold in multiples of 25. Let's say you want to buy a bunch of 18" oval link chains. If you buy one 25 pack in silver you get a 3% discount but if you buy 3 more 25 packs in any other color you'll now get 100 18" chains at the 10% wholesale discount. If you buy a total of 250 18" oval link chains (any color combo) you qualify for the 20% off rate. In other words, the discount you get is based on each item.
On glass the discount applies to each size and shape. So if you order 100 25mm round cabs (4 25 packs) you get the 10% discount on them and if you add 25 30mm round cabs (1 25 pack) you get the 3% discount on those.
If this is confusing we advise you play with your cart by adding and subtracting items. This model could change down the road but we think using discounts across the product and not each variant is best for our customers.