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The observed discrepancy in the light output, measured for a number of LSO, LYSO and BGO scintillators by different photomultipliers (PMTs), triggered studies to understand the problem. For that purpose the photoelectron number was measured by two different methods: the direct one based on a comparison of the full energy peak to that of the single photoelectron and by a method based on the pulse height resolution of the peak due to the light pulser. In this study, a significant number of different PMTs from Photonis and Hamamatsu were used. We concluded that the number of photoelectrons measured by means of the direct method was higher than the number of photoelectrons calculated from the pulse height resolution of the light pulser peak for all of the PMTs but XP2020Q. It leads to a large dispersion in the estimated light output for a given scintillator. In detail, the light output of BGO and LSO determined with the R6231 and R2059 PMTs is comparable to those measured with XP2020Q PMT and the S3590-18 pin photodiode, when photoelectron number is calculated from the pulse height resolution. Further in-depth studies of the photoelectron number at different bias voltages suggested that the effect is related to the space charge created in the dynode structure of the PMTs. Operation of PMTs at lower bias/gain minimizes this effect; thus, low noise electronics are recommended to determine the single photoelectron peak under these conditions. Moreover, the absolute light output of scintillators is affected by differences in the quantum efficiency calibrations by Photonis and Hamamatsu.