The next generation of critical systems, namely complex Critical Infrastructures (LCCIs), require efficient runtime management, reconfiguration strategies, and the ability to take decisions on the basis of current and past behavior of the system. Anomaly-based detection, leveraging information gathered at Operating System (OS) level (e.g., number of system call errors, signals, and holding semaphores in the time unit), seems to be a promising approach to reveal online application faults. Recently an experimental campaign to evaluate the performance of two anomaly detection algorithms was performed on a case study from the Air Traffic Management (ATM) domain, deployed under the popular OS used in the production environment, i.e., Red Hat 5 EL. In this paper we investigate the impact of the OS and the monitored resources on the quality of the detection, by executing experiments on Windows Server 2008. Experimental results allow identifying which of the two operating systems provides monitoring facilities best suited to implement the anomaly detection algorithms that we have considered. Moreover numerical sensitivity analysis of the detector parameters is carried out to understand the impact of their setting on the performance.