This paper discussed an architecture-led approach to diagnosing time sensitive issues with a stepper motor controller that manages fuel flow of an engine. A real engine control system design had originally been modeled and verified with SCADE . The potential for missed steps that result in misalignment in the fuel valve position is difficult to test for and was not discovered until after the engine went into operation. We utilize the execution and communication timing semantics of AADL to architecturally characterize the interaction between the elements of the stepper motor control systems. We then characterize the functional behavior in the context of the task dispatch and input handling semantics using the AADL Behavior Annex and identify potential fault sources and their impact using the AADL Error Model Annex. The identified the potential error sources, early arrival and mismatched command rates, we quantify the condition for this to occur and analyze the system based on timing data from scheduling analysis and actual timing measurements. We use this analysis to evaluate several proposed design corrections.