Reasoning Instructions Can Break Answer Decoding in Vision--Language Models

arXiv:2609.29278v1 Announce Type: new Abstract: Chain-of-thought (CoT) instructions can distort multiple-choice VLM evaluation when a scorer appends a reasoning cue but reads answer-label logits before the model generates any rationale. We call this CoT-prefix scoring. On ScienceQA, Qwen2.5-VL-7B drops from 80.76% to 45.48%, and across five option-content permutations 93.54% of CoT-prefix predictions select the first slot. Condition-matched linear probes recover 78.94% from the same hidden states, while free generation restores 75.24%, showing that the answer often survives the prefix and the immediate readout fails. Vocabulary and layer diag