I take it you are cooling two CDs with one pump. Apply the conservation of mass. With one source of flow and pressure you must evenly split (divide) the flow between the two coolers. That means the same diameters, lengths, and fittings on the two parallel lines. The pump output is also divided evenly. If you have a design that requires a certain flow rate, the "rule of thumb" is to choose a pump design where the design point is 75% of the pump rating.
The heat transfer problem may be inadequate contact between the CD and the cooler.
I would recommend that you tackle one problem at a time, eliminating each one until the real culprit is found.
Merle Jephson-King