The role of proton transfer in the photoluminescence intermittency (PI) of single molecules of violamine R (VR) overgrown in potassium acid phthalate (KAP) crystals is evaluated in comparisons of protonated (KAP) and deuterated (DKAP) mixed crystals between 23 and 60 °C. The PI is analyzed by the construction of cumulative distribution functions that are statistically compared. We find that the on- and off-interval duration distributions change with isotopic substitution consistent with proton transfer contributing to the PI of VR. The on- and off-interval duration distributions have distinct temperature dependencies consistent with different mechanisms for dark state production and decay. Additional evidence for proton-transfer is provided by distributions of single molecule emission-energy maxima that reflect emission from protonated and deprotonated VR. A mechanism for the PI of KAP is presented, where the dark state is assigned to formation of the colorless, leuco form of VR, formed by proton transfer from VR to the KAP lattice, and decay of the dark state involves ring-opening promoted by proton transfer from KAP to VR. The distributed kinetics for dark-state production and decay are modeled using a log-normal distribution for the PI data in preference to a power-law previously assumed. A discussion of the log-normal distribution with regards to PI and proton transfer is presented.