Structure-factor extractions in commonly used Rietveld refinement programs (FullProf, Jana2006 and GSAS) were examined with respect to subsequent calculation of electron-density distributions (EDDs) using the maximum entropy method (MEM). As a test case, 90 K synchrotron powder X-ray diffraction data were collected on the potential hydrogen storage material, NaGaH(4), at SPring-8, Japan. To support the model, neutron powder diffraction data were collected on the fully deuterated sample at PSI, Switzerland. Firstly, it was established whether the programs can produce observed structure factors, F(obs), corrected for anomalous dispersion and scaled to the scattering power of one unit cell. Secondly, different models for background and peak-shape description were investigated with respect to the extracted F(obs), and the effect on the subsequent MEM EDDs was analysed within the quantum theory of atoms in molecules. Substantial differences are observed in the estimated standard deviations, σ(obs), produced by the different programs. Since σ(obs) is a vital parameter in the calculation of MEM EDDs this leads to substantial variation between the MEM EDDs obtained with different Rietveld programs even in cases with similar F(obs). A new approach for selecting an optimized MEM EDD and thereby minimizing the effect of variation in σ(obs) is suggested.