To answer your question, no i never had that problem. What i done was plugged the fans into the cpu fan header and the plugged the pump that sits on the cpu into the system fan header. As shown in the below.
I am going to be changing my motherboard even though its a month old. I decided to purchase a motherboard that supports water cooling with the correct headers.
By the way you need to try and sort out your cable management, it is a mess and restricting air flow through the case. I done my best to open up airflow as possible as there only so much you can do with tucking cables away.