You may still have a significant pocket of air trapped somewhere in the loop, likely in a radiator(s).
Air likes to collect in the radiator(s) because the water flow splits into multiple parallel flow paths through them, greatly reducing the velocity, which allows small and micro bubbles to escape the flow and form a large bubble in the plenum chambers of the radiator.
If you have a top mounted radiator, this is an especially common issue.
If you have your MCP35x pumps set up to run at a low PWM setting at idle and light usage temps, the flow velocity is very low through the radiator(s), which helps air collect there.
When the pumps speed up, the flow velocity increases, and some of the air gets entrained back into the flow.
Try kicking your pumps up to 100%, and laying the case all the way onto its side, preferably with the outlet port of the radiator higher than the inlet port.
Be sure that water will still be above the reservoir outlet to the pump when the case is on its side though.
Get physics working for you instead of against you.
With my rig, I find that it helps to let the pumps run at a low speed for a while to allow larger bubbles to form, then bump them up to 100% for a couple of minutes to push the big bubbles out.
Alternatively, if your temperatures are good, don't worry about the bubbles, they will eventually work themselves out.
Windfire's advice to set up a 2 step speed profile is pretty good, it is how I have mine set, but I use Speedfan.
It avoids the constant ramping up and down you get if they are following a curve.
The Asus software is extremely easy to use, but doesn't allow for as low of a minimum speed as Speedfan, and only allows for a user defined profile for one of the PWM fan headers.
I'm using Speedfan to control my pumps and my fans off separate headers.
Speedfan offers much more options than the Asus software, but is orders of magnitude more complex to learn and set up.
2 MCP35x pumps run off the PWM fan header on my GTX470 video card.
9 Akasa Viper fans run off the CPU PWM fan header.Edited by Caleal - 2/26/12 at 7:51am