Have you confirmed that the order is being entered within the valid date range of the contract price for the item?
 
We use contract prices quite a bit. Once in a while they won't pull in for some unknown reason. But, if you do a <F2> lookup in the price field of the SO, it shows the correct pricing.

I have gone into SO-Q-H to try to enter contract prices, and it isn't working, so there seems to be something up with the module.  I am going to report it in the repeatable issues.
Ann Luce

Hello, David,
I submitted a repeatable problem report, but long story short, there is apparently a problem with the module. It does not allow either an edit of an existing customer and item price, or setting a new one. In an edit, it starts with a particular customer and will not change, and in an edit and a new creation, it just jumps the contract price box, and goes right to the base prices area. Perhaps it garbled in the download of a program update or patch batch. 'Tis a puzzlement.
Ann