Hi Jerry,
please check the pricing procedure for conditions. If all ok then would say its bad behavior of the system at the time of pricing determination of the document .
You can re-determine the pricing procedure on the web ui. there suppose to be an a button available on the Web Ui just above the pricing assignment block you need to click on that then system will re-pricing it and hopefully your issue will be solved. I had faces the same situation long back in my project and have solved it like this way only.
Thanks,
Prem