As you have discovered, the budget cost and budget work field are "top down" estimates and can only be applied to the Project Summary task.

As you have more detailed estimated, I suggest adding the Fixed Cost field to the Gantt chart view and entering the values there. Then you can save a baseline after all planning is complete and have a "baseline" cost for comparison once you start tracking. The "baseline cost" is frequently referred to as the "budget".

Regarding the odd numbers - what version of Project and what service pack is applied?