We had Two Rinnai R98s in series to get us to the flow rate we needed for our 15bbl brewhouse. We began to experience exactly what you are talking about and discovered two things
1. We had just done some plumbing and the plumber had made a mistake and the cold water was backflushing into the hot water. But based upon his mistake it only happened when someone was using our mop sink. So make sure your hot and your cold are completely separated.
2. Once we fixed the above we still had the problem but not as severe. So we also had a tech come in to inspect the older of the two systems. He took it apart, showed me the heat exchanger and declared that it was toast. The system had to be replaced. So we took it off and installed a much more robust on demand in its place. We got 2.5 years out of the Rinnai and the tech said he had never seen a Rinnai more worn out than this one. Compared it to being in a house for 20 years.
Good luck, I understand the frustration with having your on demand go in and out on you. Makes brewing difficult.