Inverse Gas Chromatography (IGC) is an established technique for the determination of the surface energy heterogeneity of various types of materials, including particulate and fibrous materials. However, variability in sample and column preparation may lead to low reproducibility of data. In this work, the influence of two aspects of chromatographic column preparation; the amount of silanised glass wool and the packing structure of mixtures of particulate materials, on IGC measurements were investigated using a combined experimental and modelling approach. In silico experiments were used to examine these factors for a range of materials with different surface energy. We report here, that the packing structure of particulate materials in the column does not significantly affect the measurements and the results. However, the contribution of the silanised glass wool needs to be corrected, particularly for materials of low surface area or low surface energy. This work demonstrates the importance of column preparation and the need for standardisation of packing protocols for robust experimental determination of surface energy heterogeneity.