Large language model (LLM) agents with extended autonomy unlock new capabilities, but also introduce heightened challenges for LLM safety. In particular, an LLM agent may pursue objectives that deviate from human values and ethical norms, a risk known as value misalignment. Existing evaluations primarily focus on responses to explicit harmful input or robustness against system failure, while value misalignment in realistic, fully benign, and agentic settings remains largely underexplored. To fill this gap, we first formalize the Loss-of-Control risk and identify the previously underexamined Intrinsic Value Misalignment (Intrinsic VM). We then introduce IMPRESS (Intrinsic Value Misalignment Probes in REalistic Scenario Set), a scenario-driven framework for systematically assessing this risk. Following our framework, we construct benchmarks composed of realistic, fully benign, and contextualized scenarios, using a multi-stage LLM generation pipeline with rigorous quality control. We evaluate Intrinsic VM on 21 state-of-the-art LLM agents and find that it is a common and broadly observed safety risk across models. Moreover, the misalignment rates vary by motives, risk types, model scales, and architectures. While decoding strategies and hyperparameters exhibit only marginal influence, contextualization and framing mechanisms significantly shape misalignment behaviors. Finally, we conduct human verification to validate our automated judgments and assess existing mitigation strategies, such as safety prompting and guardrails, which show instability or limited effectiveness. We further demonstrate key use cases of IMPRESS across the AI Ecosystem. Our code and benchmark will be publicly released upon acceptance.