Distributed tracing in large-scale AI infrastructure fails silently when clock accuracy is insufficient: causal events are misordered, fault attribution is corrupted, and performance diagnoses are unreliable. We present TempoTrace, a system that co-designs IEEE 1588v2 PTP time synchronization with distributed tracing to preserve causal ordering across heterogeneous, multi-tenant GPU clusters. We formally prove that NTP-grade clocks produce causal inversions at 25-30% of directed operation pairs under WAN/cloud conditions (11.3% under LAN NTP). A Laplace heavy-tail noise model extends the analysis beyond Gaussian assumptions, giving a weighted expected misorder rate of 27.76% vs. 29.37% Gaussian, confirming robustness to tail shape. TempoTrace reduces GPU-to-host timestamp uncertainty from 2.1 us to a design target of 0.056 us residual standard deviation via GPUDirect RDMA hardware timestamping, with sub-100 ns PTP synchronization. A bounded Sketch Vector Clock tracks causal relationships with false-positive rate below 10^-5 for up to four participants. A hybrid rule-based and XGBoost diagnosis engine achieves macro-F1 0.974 in controlled validation (1,800-incident corpus; McNemar p=1.25e-23). A formally proven multi-tenant model provides isolated logical clock domains. For RoCEv2/ECMP fabrics, P4-based in-band network telemetry corrects path-delay asymmetry, yielding 99.1% attribution accuracy. Application Confidence Policies let workloads specify precision requirements and degraded-mode fallback. Evaluation combines physical five-node measurements (NTP inversion rate 44.978%, Laplace fit preferred over Gaussian by AIC under congestion) and controlled synthetic validation with illustrative configurations from 512 to 16,384 H100 GPUs across InfiniBand and RoCEv2 fabrics.

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