When Do LLM Agents Treat Surface Noise Differently from Semantic Noise? A 68-Cell Measurement Study with a Held-Out Trace-Level Validation

We document an empirical phenomenon in chain-of-thought and ReAct agents driven by ten large language models from seven architecture families: meaning-bearing perturbations (e.g., paraphrase, synonym) alter final answers more often than presentation perturbations (e.g., formatting, reordering) of comparable severity. Across 68 cells spanning GSM8K, MATH, and HotpotQA (1,530 originals and $\sim$11,150 variants), the inconsistency gap averages +19.69 pp after severity matching (paired $t=9.58$, $p<0.0001$), with 64/68 cells positive. The gap survives four severity-proxy audits and remains significant when excluding qwen models (+11.10 pp, $p<0.0001$). Several stress tests fail honestly: cluster-bootstrap significance disappears under stricter assumptions, tractability contrasts do not replicate, cross-architecture generator swaps break per-cell rankings, and a second LLM judge yields only moderate agreement ($κ=0.50$). We then validate the headline effect on a fully held-out 11th model (qwen2.5-14B-Instruct; 1,800 trajectories) and re-test a pre-registered capability$\times$tractability partition, observing a small but positive held-out effect (3/4 cells positive; pooled Welch $t=3.81$, $p=9.6\times10^{-4}$). Using held-out trajectories, we probe four trace-level mechanism signals. Two prior mechanism claims fail to replicate and are explicitly retracted. Two new probes instead support a \emph{stealth-divergence} picture: semantic perturbations often preserve the first action but induce divergence in intermediate reasoning from later steps onward, accompanied by slightly deeper trajectories. We position this as a measurement contribution with held-out replication and a partial trace-level account of how semantic perturbations propagate through agent reasoning. Code, perturbation corpus, raw trajectories, and analysis scripts are released anonymously for review.