When do merchants start paying the actual value of items without bonus effects and perks?

Solution 1:

Sounds like you have low Speech

Speech will directly affect the prices paid when buying from and selling to merchants, even without the assorted perks. At 0 speech, merchants will sell items for 3 times their base price, and buy for a third of their base price. At 100 speech, merchants will sell items for twice their base price and buy for half.

Solution 2:

The value in your inventory is the worth of the item. Vendors will give you a percentage of that value based on your speechcraft skill and other factors. Likewise they will sell it for a multiple of that value.

Specifically the price is:

Sell price = [ value of item ] / [ 3.3 - (1.3 * [speech skill]/100) ] 
           * [(1 + Haggling %) * (1 + Allure %) * (1 + Fortify Barter from potion) 
           * (1 + the sum of Fortify Barter from equipment + Fortify Barter from Blessing of Zenithar)

From the UESP Wiki.