Issue: The store is set to use UPS negotiated rates for its shipping calculation, but returned rates are higher than they should be.
Likely Causes: Check to see if A) Negotiated rates are enabled, B) if your products might have a markup or C) if your shipping methods might have their own markups.
If your negotiated rates are not displaying correctly, check to ensure your store is set to use them, then make sure there are no markups on either the product or the shipping method.
A) Check if negotiated rates are enabled
Go to Settings > Shipping,
Then click on Enter Settings under Shipping Settings,
Click on Show Credentials for UPS.
Make sure the Use account discounted rates is marked.
B) Product Shipping Markup
Go to Products > Product List and locate the item you want to edit.
Click on the item's name, ID or thumbnail image to open it.
While viewing the product's Information tab, look under "Shipping Options" and ensure there are no markups.
Repeat for all your products as needed.
C) Shipping Method Markup
Go to Settings > Shipping.
Then click on Select Methods under Shipping Methods.
Click on Settings for each of your configured UPS methods.
Make sure there are no markups for any of them.