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

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 diagnostics explain the mismatch: probability mass moves toward continuation tokens, while answer information remains linearly accessible in late layers. The effect recurs with varying severity across datasets and models, though not universally. These results show that CoT-prefix scoring can confound model knowledge with an evaluation-interface mismatch and should be avoided unless the requested and scored output events are aligned.