I've never had that issue. I assume you have the pump heads positioned with the inlet side pointing to the floor and the outlet side pointing up? This orientation promotes air evacuating through the outlet. I've also been instructed to never restrict the inlet flow, only the outlet flow. That said, the valves on the kettles can be standard of full port types, with standard ports having a smaller diameter in the ball portion of the valve, which can lead to restricted flow. Some people use 3/4" tubing instead of 1/2" so they can use full 1/2" ID fittings as well. Wish that there was an easy to regulate pump rpm. I guess if none of these solved your issues, then hard plumbing might be your next approach. Are you thinking that the air is being sucked in along the tubing pathway someplace? I imagine that with boiling hot wort its probably the worst scenario, but for me at least, I am rarely pumping boiling hot wort.
TD