Distributed network emulators allow users to perform network evaluation by running large-scale virtual networks over a cluster of fewer machines. While they offer accessible testing environments for researchers to evaluate their contributions and for the community to reproduce its results, their use of limited physical network and compute resources can silently and negatively impact the emulation results. In this paper, we present a methodology that uses linear optimization to extract information about the physical infrastructure from emulation-level packet delay measurements, in order to pinpoint the root causes of emulation inaccuracy with minimal hypotheses. We evaluate the precision of our methodology using numerical simulations, then show how its implementation performs in a real network scenario.