The increased use of flexible manufacturing systems to provide customers with diversified products efficiently has created a significant set of operational challenges for managers. This technology poses a number of decision problems that need to be solved by researchers and practitioners. In the literature, there have been a number of attempts to solve design and operational problems. Special attention has been given to machine loading problems, which involve the assignment of job operations and allocation of tools and resources to optimize specific measures of productivity. Most existing studies focus on modeling the problem and developing heuristics in order to optimize certain performance metrics rather than on understanding the problem and the interaction between the different factors in the system. The objective of this paper is to study the machine loading problem. More specifically, we compare operation aggregation and disaggregation policies in a random flexible manufacturing system (FMS) and analyze its interaction with other factors such as routing flexibility, sequencing flexibility, machine load, buffer capacity, and alternative processing-time ratio. For this purpose, a simulation study is conducted and the results are analyzed by statistical methods. The analysis of results highlights the important factors and their levels that could yield near-optimal system performance.