I am not sure that this is a quality issue.
The difference is, that usually vendors offer a discount, if you buy cases in bulk.
But CustomGameCases only offers discounts on some of their blank cases, not all of them, for whatever reason.
NES, SNES and N64 cases cost the same no matter how many you buy. ($3,00 for 1 case, $300 for 100 cases.)
While their PSP cases (and I remember Gameboy cases as well) get cheaper, if you buy in bulk. ($2,50 for 1 case or $120 for 100 cases. So if you buy in bulk, the price drops to $1,20 per case or less then half of the original price...)