Multimodal large language models (MLLMs) excel at vision-language tasks such as VQA and document understanding, yet precise coordinate prediction remains challenging. High-resolution inputs exacerbate this difficulty by producing long token sequences that weaken positional encodings and introduce directional biases in coordinate outputs. We investigate this phenomenon by analyzing how MLLMs behave when visual positional encodings (VPEs) are deliberately perturbed through shuffling. Our analysis reveals that such perturbations induce predictable, non-random coordinate biases rather than random errors, suggesting that models rely on internal positional priors when spatial grounding signals are degraded. Crucially, we observe similar directional error patterns in natural high-resolution datasets, indicating that positional encoding failures are a key bottleneck for accurate coordinate prediction at scale. To address this issue, we propose Vision-PE Shuffle Guidance (VPSG), a training-free test-time method that leverages the directional nature of these biases for correction. VPSG runs auxiliary decoding with shuffled VPEs to isolate position-unconditioned tendencies, then uses this as negative evidence to guide digit prediction while preserving coordinate format through a lightweight finite-state machine. Experiments on ScreenSpot-Pro demonstrate reliable improvements, highlighting positional encoding robustness as a critical factor for spatial reasoning in MLLMs.