This paper investigates the application of particle swarm optimization (PSO) to the multi-objective flexible job shop scheduling problem with sequence-dependent set-up times, auxiliary resources and machine down time. To achieve this goal, alternative particle representations and problem mapping mechanisms were implemented within the PSO paradigm. This resulted in the development of four PSO-based heuristics. Benchmarking on real customer data indicated that using the priority-based representation resulted in a significant performance improvement over the existing rule-based algorithms commonly used to solve this problem. Additional investigation into algorithm scalability led to the development of a priority-based differential evolution algorithm. Apart from the academic significance of the paper, the benefit of an improved production schedule can be generalized to include cost reduction, customer satisfaction, improved profitability, and overall competitive advantage.