One of the challenges to the sustainability of the Solar Home System (SHS) electrification program in South Africa is equipment theft. In response to this, communities susceptible to solar panel theft resort to mounting their panels flat on the ground so they can be looked after during the day and taken indoors at night for safe keeping. Other households use their security lights to illuminate their environment and provide security for pole and roof mounted solar panels at night. These actions have consequential effects on the performance of the SHS. Several studies have detected resentment from households regarding the low power quality from these systems. Most scientific contributions on the issue of low power from SHS have focused on the challenges based on the technical designs of the systems. The power losses due to the usage pattern of the system has not received much attention. This study therefore reports on the technical losses as a result of the deviation from the designed and installed specification of the system by the users in order to protect their systems. It also investigates the linkage between the technical and economic losses which affects the sustainability of SHS program. A case study was performed in Thlatlaganya village within Limpopo province in South Africa. Technical analysis using PVSYST solar software revealed that the energy output and performance of the battery is compromised as a result of these practices. Economic analysis indicates that the battery life and the economics of owning and operating SHS are affected negatively. The study recommends solutions to mitigate these losses, and proposes a cost effective way of optimizing the operation of SHS using a Bench-Rack system for mounting solar panels.