Im sure one side of the loop will have slightly higher pressure than the other. Dont forget that the pump will have the most effect on water pressure at the outlet connector on the pump - there shouldnt be a huge difference throughout the system.
I suspect the vibration maybe coming from the pump and not the pressure.
Bit like the human heart - blood pressure has two levels the upper figure is the fresh supply leaving the heart.... lower one is the blood returning.
You cooling loop works the same way.
If the temperatures are stable I wouldnt worry too much - just try and damped the pump mount to reduce vibration (make sure you have no kinks also)