I believe it may have nothing to do with ion exchange chemistry. The softener may be experiencing organic fouling, releasing acids either from bacteria or organic chemicals. You can verify the guess by sampling a column of resin for microscopic examination and a caustic rinse wash.
Another factor I forgot to bring up is bacteria. I don't know the operating temperature. If the temperature is below 120 F, you may have anaerobic bacteria problem. In other words, acid producing bacteria may be present in your system.
pH 5.5 is corrosive to copper. Ideal pH for copper is between 7.5 and 9.3. If you should use antifreeze, don't use automotive grade antifreeze because it contains silicate. Silicate is unstable in low pH. It forms gels and fouls your heat exchanger. If you use water, you can buy corrosion...
A comprehensive water analysis should be done, at least on one of the low pH (~4) samples to diagnose the problem. My guess is something to do with the pretreatment of the RO. If you can break down the cations and the anions in the water analysis, it will shed more light to the problem.