Probably it is indeed your configuration. The loot is valued according to the price set in your cyclopedia. So if, e.g., the price of the dreaded cleaver is set to 15k, selling on Alesar, but you sell it on Rashid, for 10k, you'll have less profit than estimated. The same applies to itens items which value is set to market value but you sell on NPC's for a lower value.