Fuel assemblies in the spent fuel pool are stored by suspending them in two vertically stacked layers at the Atucha Unit 1 nuclear power plant (Atucha-I). This introduces the unique problem of verifying the presence of fuel in either layer without physically moving the fuel assemblies. Given that the facility uses both natural uranium and slightly enriched uranium at 0.85 wt% 235U and has been in operation since 1974, a wide range of burnups and cooling times can exist in any given pool. A gross defect detection tool, the spent fuel neutron counter (SFNC), has been used at the site to verify the presence of fuel up to burnups of 8000 MWd/t. At higher discharge burnups, the existing signal processing software of the tool was found to fail due to nonlinearity of the source term with burnup. A new software package based on the LabVIEW platform was developed to predict expected neutron signals covering all ranges of burnups and cooling times. The algorithm employed in the software uses a set of transfer functions that are coupled with source terms based on various cooling times and burnups for each of the two enrichment levels. The software was benchmarked against an extensive set of measured data. Overall, out of 326 data points examined, the software data deviated from the measured data <10% in 87% of the cases. A further 10.5% matched the measurements between 10% and 20%. Thus, 97.5% of the predictions matched the measurements within the set 20% tolerance limit providing proof of the robustness of the software. This software package linked to SFNC will enhance the capability of gross defect verification at both levels in the spent fuel pool for the whole range of burnup, cooling time, and initial enrichments of the spent fuel being discharged into the various pools at the Atucha-I reactor site.