Hey,
I haven't used the budget analyzer for heat fluxes, but what you described sounds familiar from flow budgets. As far as I know, FeFlow calculates flows into a multi-layer well based on the layers' transmissivities, but only reports the flow total in the water budget at the node where a BC value <> 0 was specified. During the simulation, however, that total is spread along the well segment, so that ALL BC nodes along the well receive some portion of the total flow. Can someone confirm that??? It is confusing though ...
Chris.