I only can think that you get a higher resistance because of turbulences when the water 'tries' to get through the fins. The fins at the beginning are not round or aquadynamic and the resulting little turbulences blocking the flow through the fins and the result is a higher resistance. The restistance through the smaller lower channel seems to be lower and the water flows that way. I guess it's much more distinctive if you have low water pressure or flow rate.
You must consider, that your old water blocks didn't have that detour to the voltage converters.
Did you try to max. the RPM of your pump yet? Perhaps a higher flow rate leads to a better flow through the fins and grooves?