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We introduce a method to isolate faults at run-time in an embedded system whose components form a matrix structure. Our method probes a system via test paths a SAT-solver recommends, feeding the SAT-solver with the encodings for test path conditions and the current status of the system. After receiving test results, the SAT-solver recommends another test path suitable for the situation. We can detect all defects by checking the system until the SAT-solver does not make any useful suggestions. Our SAT-based fault diagnosis ensures termination and conducts only essential inspections without misses of potential flaws.