So I redid some of my reactors, and added a fuel type specifically for them which are considerably smaller and cheaper than basic He3 rods. This results in free refueling at stations using either rin or nara economies.

 If I had to guess without source-diving, the issue is that it gets the cost for individual fuel rods first, and then multiplies that out to get the total cost. If the cost of a single fuel rod comes out to less than one for a given economy, it rounds down to zero and you get free refueling. The total cost in credits should probably to be calculated first, and then converted to the appropriate economy.