Need more info than you're giving us here. I've always gotten full refunds, but then I'm always careful about procedures and how I handle the products.
I've gotten full refunds on 2 different graphics cards, RAM, and several other components at different times over the last 3 years, most recently 2 weeks ago. Refunds were processed in a reasonable amount of time.
I was able to prove the products faulty and include documentation to that effect from the manufacturer each time. Each time I contacted manufacturer tech support to confirm it was a faulty item, then included the correspondence to NewEgg to expedite the issue.
NewEgg will take the motherboard you returned, and examine it, test it. If they determined that the motherboard was not faulty, or were not able to find the fault with the motherboard, then you may have been subject to a restocking fee. If they sent you a return shipping label, and were unable to find the fault on the motherboard, then they would have also deducted the amount of shipping from your refund as well.
If you have something from the manufacturer to show NewEgg that it is faulty, then they won't have to go through the trouble to test it, because the manufacturer is already expecting that serial number to be returned to them.
If they found burn marks on the board, then they may have determined it was damaged by you, in which case you probably wouldn't have gotten a refund at all, so that's likely not the case here.