You're misinterpreting things.
The value you receive when selling an item is a function of your relative Speechcraft skill against that of the Merchant. Thieves guild fences all have very high mercantile skill, and will give you poor prices compared to other merchants. If you visit every shopkeeper in town with your legit goods, you will notice a similar, though smaller variation in prices.
If you'd like to get a higher price for your stolen goods, invest a perk in the Fence ability near the top of the Speechcraft tree; you'll be able to sell your ill-gotten goods to other, less shrewd negotiators with that.