At the Ibaraki Neutron Medical Research Center, an accelerator-based neutron source for iBNCT (Ibaraki - Boron Neutron Capture Therapy) is being developed using an 8-MeV proton linac and a beryllium-based neutron production target. The proton linac consists of an RFQ and a DTL, which is almost the same as the front part of J-PARC linac. However, here only one high-power klystron is used as the RF source to drive the two cavities, which have quite different Q-values and responses. From June 2016, a cPCI based digital feedback system was applied to the iBNCT accelerator. It serves not only as a controller for the feedback of acceleration fields, but also as a smart operator for the auto-tuning of the two cavities in the meantime, especially during the RF startup process to the full power. The details will be described in this report.