The proton light yield of organic scintillators has been measured extensively in recent years using fast waveform digitizers and large discrepancies exist in the values reported by different authors. In this letter, we address principles of digital signal processing that must be considered when conducting scintillator light yield measurements. Digitized waveform pulse height values are only proportional to the amount of scintillation light if the temporal shape of the scintillation pulse is independent of the amount of energy deposited. This is not the case for scintillation pulses resulting from fast neutron interactions in organic scintillators. Authors measuring proton light yield should therefore report pulse integral values and ensure that the integration length is long enough to capture most of the scintillation light.