I have observed this phenomenon in piping systems which have a large compliance.  I once designed a flow loop for demonstrating check valve operation using a centrifugal pump, check valve, a tee with a ball valve and vertical leg full of air, and a ball valve on the discharge leg.  By varying the spring rate and mass (air column length, either by adjusting discharge valve or initial water level),  damping (valve position), and excitation (pump speed) we were able to get a wide range of flow oscillations up to significant back flow through the pump causing rapid closure of the check valves, and oscillation periods of from fractions of a second to several seconds.

While I have never seen any references to this in any books, my guess is that you have gas in your system, or possibly pulsation dampers that are undercharged, and it is acting like a spring-mass oscillator with the pump acting as the excitation force.  Heat exchangers can also have a large amount of flexure if there are enough tubes.  You might also check for pressure relief devices that are set too low.

Chilled water systems driven with centrifugal pumps will often display surging pressure when the pump is running beyond its BEP best efficiency point.  Look at the pump performance curve and the discharge pressure, if discharge pressure is less the the discharge pressure at the BEP, this could be you problem. If you can throttle the system (without restricting the cooling) perhaps this would help.  The best solution is choose the pump to that you operate at or very close to the BEP.