IAEA Soil-6 is a reference material with a certified value for 226Ra fall between 69.6 – 93.4 Bq/kg at 95% confidence level. This material has been used as a sample and performed repeat measurement weekly between years 2006 – 2009 using a same gamma spectrometry system. The activity concentration of this material is calculated automatically using the operational commercial software and compared with activity obtained from the manual calculation. Study found that only 76.9%, 64.1%, 56.3%, and 79.3% of the results from the software calculation lie within the confidence level for year 2006, 2007, 2008 and 2009, respectively. However, u-score calculation revealed that 94.9 %, 89.7%, 79.2% and 84.9% data set have no significant bias (u < 2.58) for year 2006, 2007, 2008 and 2009, respectively. On the other hand, all manual calculation data were found to be within the 95 % confidence level. Factors suspected to cause differences between these two approaches were discussed here. Manually peak search, marking and calculation still remains as the preferred option for calculating the gamma radionuclides activity unless limitations of the spectrum analysis software, as described in this paper can be resolved/improved upon.