Large Vision Language Models (LVLMs) excel in various vision-language tasks. Yet, their robustness to visual variations in position, scale, orientation, and context that objects in natural scenes inevitably exhibit due to changes in viewpoint and environment remains largely underexplored. To bridge this gap, we introduce V$^2$R-Bench, a comprehensive benchmark framework for evaluating Visual Variation Robustness of LVLMs, which encompasses automated evaluation dataset generation and principled metrics for thorough robustness assessment. Through extensive evaluation on 21 LVLMs, we reveal a surprising vulnerability to visual variations, in which even advanced models that excel at complex vision-language tasks significantly underperform on simple tasks such as object recognition. Interestingly, these models exhibit a distinct visual position bias that contradicts theories of effective receptive fields, and demonstrate a human-like visual acuity threshold. To identify the source of these vulnerabilities, we present a systematic framework for component-level analysis, featuring a novel visualization approach for aligned visual features. Results show that these vulnerabilities stem from error accumulation in the pipeline architecture and inadequate multimodal alignment. Complementary experiments with synthetic data further demonstrate that these limitations are fundamentally architectural deficiencies, scoring the need for architectural innovations in future LVLM designs.