Reliable evaluation is fundamental to the progress of Large Language Models (LLMs), yet the evaluation process during pre-training is plagued by significant instability that obscures true learning dynamics. In this work, we systematically diagnose this instability, attributing it to two distinct sources: \textit{Parameter Instability} from training stochasticity and \textit{Evaluation Instability} from noisy measurement protocols. To counteract both sources of noise, we introduce \textbf{MaP}, a dual-pronged framework that synergistically integrates checkpoint \underline{M}erging \underline{a}nd the \underline{P}ass@k metric. Checkpoint merging smooths the parameter space by averaging recent model weights, while Pass@k provides a robust, low-variance statistical estimate of model capability. Extensive experiments show that MaP yields significantly smoother performance curves, reduces inter-run variance, and ensures more consistent model rankings. Ultimately, MaP provides a more reliable and faithful lens for observing LLM training dynamics, laying a crucial empirical foundation for LLM research.