Embedded Controllers form a vital part of the industrial control system. The typical implementation of such controller is around a multitasking kernel which periodically executes the control and systems tasks. Delay in the control task execution can lead to jitter and unexpected behavior of the system under control. In this paper we investigate the case of malicious attacks on the scheduler and its effect on jitter. TRUETIME, a Simulink based simulator was used for simulation of jitter in real time control system.