Our understanding of physical processes in photodissociation regions or photon-dominated regions (PDRs) largely depends on the ability of spectral synthesis codes to reproduce the observed infrared emission-line spectrum. In this paper, we explore the sensitivity of a single PDR model to microphysical details. Our calculations use the Cloudy spectral synthesis code, recently modified to include a wealth of PDR physical processes. We show how the chemical/thermal structure of a PDR, along with the calculated spectrum, changes when the treatment of physical processes such as grain physics and atomic/molecular rates are varied. We find a significant variation in the intensities of PDR emission lines, depending on different treatments of the gr...