Hi Zanie -
Check under Basic Params: Costs, and verify that the Cost-Benefit Calculation Boundary is set appropriately (or that you have not recently accidentally changed it). If this excludes one or more transformation modules, then you will not see costs entered within these modules when you view results.
This page gives a few more details about the cost-benefit boundary:
http://www.energycommunity.org/WebHelpPro/Concepts/Transformation_Cost_Calculations.htm
Also verify that costs are enabled for each relevant transformation module, in their module properties.
Hope this helps,
Taylor