Many software projects are configurable through compile-time options (e.g., using ./configure) and also through run-time options (e.g., command-line parameters, fed to the software at execution time). Several works have shown how to predict the effect of run-time options on performance. However it is yet to be studied how these prediction models behave when the software is built with different compile-time options. For instance, is the best run-time configuration always the best w.r.t. the chosen compilation options? In this paper, we investigate the effect of compile-time options on the performance distributions of 4 software systems. There are cases where the compiler layer effect is linear which is an opportunity to generalize performance models or to tune and measure runtime performance at lower cost. We also prove there can exist an interplay by exhibiting a case where compile-time options significantly alter the performance distributions of a configurable system.