A critical aspect of software development, build reproducibility, ensures the dependability, security, and maintainability of software systems. Although several factors, including the build environment, have been investigated in the context of non-reproducible builds, to the best of our knowledge the precise influence of configuration options in configurable systems has not been thoroughly investigated. This paper aims at filling this gap. This paper thus proposes an approach for the automatic identification of configuration options causing non-reproducibility of builds. It begins by building a set of builds in order to detect non-reproducible ones through binary comparison. We then develop automated techniques that combine statistical learning with symbolic reasoning to analyze over 20,000 configuration options. Our methods are designed to both detect options causing non-reproducibility, and remedy non-reproducible configurations, two tasks that are challenging and costly to perform manually. We evaluate our approach on three case studies, namely Toybox, Busybox, and Linux, analyzing more than 2,000 configurations for each of them. Toybox and Busybox come exempt from nonreproducibility. In contrast, 47% of Linux configurations lead to non-reproducible builds. The approach we propose in this paper is capable of identifying 10 configuration options that caused this non-reproducibility. When confronted to the Linux documentation, none of these are documented as non-reproducible. Thus, our identified non-reproducible configuration options are novel knowledge and constitutes a direct, actionable information improvement for the Linux community. Finally, we demonstrate that our methodology effectively identifies a set of undesirable option values, enabling the enhancement and expansion of the Linux kernel documentation while automatically rectifying 96% of encountered non-reproducible builds.