Sounds like maybe a faulty fan..If you have another fan, like from your old Corsair cooler, you could plug it into the fan Y-Splitter coming from the pump unit (which controls the fans) and see how it works..Or, plug the EVGA cooler fan into a motherboard fan header and see how it works.
If you RMA the cooler assembly to EVGA, you'll have to pay the shipping to them and they'll pay the return shipping back to you..Keep that in mind because if it's just a faulty fan, you might be able to buy new/better fans for what it would cost you for shipping..Maybe try using the fans from your Corsair cooler or other fans you might have laying around and see how it works?
The pump/fans should work fine without any software (Flow Control) intervention..You could uninstall Flow Control and see how it works.
Just a few things here.