Chain-of-Thought reasoning is widely used to improve the interpretability of multimodal large language models (MLLMs), yet the faithfulness of the generated reasoning traces remains unclear. Prior work has mainly focused on perceptual hallucinations, leaving reasoning level unfaithfulness underexplored. To isolate faithfulness from linguistic priors, we introduce SPD-Faith Bench, a diagnostic benchmark based on fine-grained image difference reasoning that enforces explicit visual comparison. Evaluations on state-of-the-art MLLMs reveal two systematic failure modes, perceptual blindness and perception-reasoning dissociation. We trace these failures to decaying visual attention and representation shifts in the residual stream. Guided by this analysis, we propose SAGE, a train-free visual evidence-calibrated framework that improves visual routing and aligns reasoning with perception. Our results highlight the importance of explicitly evaluating faithfulness beyond response correctness. Our benchmark and codes are available at https://github.com/Johanson-colab/SPD-Faith-Bench.