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The observed discrepancy in the scintillator light output, measured by different PMTs, triggered studies to understand the problem. In that purpose the photoelectrons number were measured by two different methods: the classical one based on comparison of the full energy peak to that of single photoelectron and by a method based on the pulse height resolution of the peak due to the light pulser. Under the test significant number of different PMTs from Photonis and Hamamatsu were used. We concluded that the number of phe obtain by means of classical method was higher than the number of phe calculated from the pulse height resolution of the light pulser peak for all of the PMTs but XP2020Q. It leads to large dispersion in the estimated light output for a given scintillator. In details, the light output of BGO and LSO determined with R6231 and R2095 is comparable to those measured with XP2020Q and S3590-18 pin photodiode, when photoelectron number calculated from the pulse height resolution is used. Further carried on in-depth studies of the photoelectron number at different HV suggested that the effect is related to the space charge created over the dynode structure of PMTs. Operation of PMTs at lower HV/gain minimizes this effect, thus low noise electronics is recommended to get the single photoelectron peak at this conditions. Moreover, the absolute light output of scintillators is affected by differences in the quantum efficiency calibration at Photonis and Hamamatsu.