Unexplored flaws in multiple-choice VQA make benchmarking unreliable

Previous works identify sensitivity to option order as a key issue in multiple-choice VQA (MC-VQA) evaluation and propose protocols to mitigate this effect. We show that such mitigation is insufficient to ensure the validity of MC-VQA as a reliable benchmark for Multimodal Large Language Model (MLLMs): performance remains highly sensitive to semantically neutral prompt format choices that are not controlled by current benchmarks. In a large-scale study spanning seven MLLMs and five MC-VQAs datasets, we find frequent rank reversals even under order-invariant evaluation. These reversals arise when we systematically vary option ID sets, delimiters, and separators, yielding 48 semantically equivalent prompt formats. Mechanistic analyses trace this instability to low-level language modeling effects: tokenizer-induced fusion or removal of option ID tokens introduces corrupted option ID tokens into the input sequence, while the choice of option ID sets directly affects the reliability of attention patterns for option selection. Accordingly, MC-VQA rankings correlate weakly with open-ended evaluation, indicating that MC-VQA reflects option-selection dynamics in addition to multimodal reasoning. These findings identify prompt formatting as a major, previously under-controlled confounder in MC-VQA benchmarking and motivate evaluation protocols that explicitly control prompt format sensitivity.