Yeah, 3 working pins mounting the cooler results in uneven pressure. Chances are, "insulating" air is getting between the mating surfaces.
It is not the number of fans that really matters, it is how they are oriented. They need to be working together to create a flow through the case. What are those bottom fans doing?
Typically, you go for front to back flow, or bottom to top (unless using a radiator). And you typically want a slight over or positive pressure (a little more coming in than being exhausted out) as that forces the air to come in through the [hopefully] filtered intake vents only. When you have under or negative pressure, unfiltered air is pulled in through every crack, crevice and port - you don't want that.