Right, I'm following you. Running at full speed for any length of time is causing too much turbulence and I'm guessing introducing bubbles into the loop, which is causing obvious problems.

Long story short, the only way to avoid this will be to not use PWM. As above, PWM will always run things at 100% on startup. Nothing you can do to change this, this is how the system is designed to work. You'll need to connect your pumps to your Lamptron controller and use direct voltage regulation instead. If you do this, you cannot also connect the 4-pin PWM wire to your motherboard unless you first disconnect the PWM wire (ie. turn the 4pin into a 3pin), otherwise your pumps will be trying to both run with less power (voltage reg) and turn on and off rapidly (PWM), which is bad both mechanically and electrically.