In this paper, we investigate how the presence of a general purpose operating system influences the reliability of modern embedded Systems-on-Chips (SoCs). We analytically study the difference in the reliability of SoCs when executing the application bare to the metal and on top of the Linux kernel. Our analysis demonstrates that Linux presence barely affects the Silent Data Corruption rate while it greatly increases the system Functional Interruption (FI) rate (up to 7.48 times) if no preventive measures are taken. Furthermore, we analytically show that cache conflicts between the operating system and application can significantly reduce the Linux-induced FI rate increase. To support our analysis, a total of four representative embedded applications were individually executed bare to the metal and on top of Linux on a 28nm ARM-based SoC exposed to an accelerated neutron beam. Our experimental results demonstrate that, by carefully tuning cache conflicts, it is possible to successfully limit the Linux-induced FI rate increase to 3.85 times. The proposed solution is general and readily applied to a broad set of applications and embedded systems.