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Fine-tuning large language models (LLMs) to adapt them for specialized downstream tasks is a common practice, yet existing methods overlook a critical issue: label preference discrepancies among different annotators. Such inconsistencies in labeling can significantly impair the model's robustness and generalization. In this work, we propose Dynamic Cross-Layer Preference Correction (DCPC), a novel self-supervised learning framework designed to mitigate these inconsistencies. DCPC incorporates a preference-sensitive similarity mechanism, cross-layer prefix alignment, and a Preference Correction Module (PCM) to dynamically adjust embeddings across transformer layers. By leveraging self-supervision, DCPC effectively aligns semantic representations and ensures consistency in label predictions, even in the presence of preference shifts. We evaluate DCPC across multiple tasks using prominent base models and introduce modified datasets that simulate real-world preference shifts. Our results show that DCPC consistently outperforms state-of-the-art Parameter-Efficient Fine-Tuning (PEFT) methods in handling label preference discrepancies.