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Large Language Models (LLMs) often exhibit tendencies that diverge from human preferences, such as favoring certain writing styles or producing verbose outputs. While crucial for improvement, identifying the factors driving these misalignments remains challenging due to existing evaluation methods' reliance on coarse-grained comparisons and lack of explainability. To address this, we introduce PROFILE, an automated framework to uncover and measure the alignment of factor-level preferences of humans and LLMs. Using PROFILE, we analyze preference alignment across summarization, instruction-following, and document-based question-answering tasks. We find a significant discrepancy: while LLMs show poor factor-level alignment with human preferences when generating texts, they demonstrate strong alignment in evaluation tasks. We demonstrate how leveraging the identified generation-evaluation gap can be used to improve LLM alignment through multiple approaches, including fine-tuning with self-guidance.