Typical evaluations of fingerprint recognition systems consist of end-to-end black-box evaluations, which assess performance in terms of overall identification or authentication accuracy. However, these black-box tests of system performance do not reveal insights into the performance of the individual modules, including image acquisition, feature extraction, and matching. On the other hand, white-box evaluations, the topic of this paper, measure the individual performance of each constituent module in isolation. While a few studies have conducted white-box evaluations of the fingerprint reader, feature extractor, and matching components, no existing study has provided a full system, white-box analysis of the uncertainty introduced at each stage of a fingerprint recognition system. In this work, we extend previous white-box evaluations of fingerprint recognition system components and provide a unified, in-depth analysis of fingerprint recognition system performance based on the aggregated white-box evaluation results. In particular, we analyze the uncertainty introduced at each stage of the fingerprint recognition system due to adverse capture conditions (i.e., varying illumination, moisture, and pressure) at the time of acquisition. Our experiments show that a system that performs better overall, in terms of black-box recognition performance, does not necessarily perform best at each module in the fingerprint recognition system pipeline, which can only be seen with white-box analysis of each sub-module. Findings such as these enable researchers to better focus their efforts in improving fingerprint recognition systems.