Purpose: Translating foundation models into clinical practice requires evaluating their performance under compound distribution shift, where severe class imbalance coexists with heterogeneous imaging appearances. This challenge is relevant for traumatic bowel injury, a rare but high-mortality diagnosis. We investigated whether specificity deficits in foundation models are associated with heterogeneity in the negative class. Methods: This retrospective study used the multi-institutional, RSNA Abdominal Traumatic Injury CT dataset (2019-2023), comprising scans from 23 centres. Two foundation models (MedCLIP, zero-shot; RadDINO, linear probe) were compared against three task-specific approaches (CNN, Transformer, Ensemble). Models were trained on 3,147 patients (2.3% bowel injury prevalence) and evaluated on an enriched 100-patient test set. To isolate negative-class effects, specificity was assessed in patients without bowel injury who had concurrent solid organ injury (n=58) versus no abdominal pathology (n=50). Results: Foundation models achieved equivalent discrimination to task-specific models (AUC, 0.64-0.68 versus 0.58-0.64) with higher sensitivity (79-91% vs 41-74%) but lower specificity (33-50% vs 50-88%). All models demonstrated high specificity in patients without abdominal pathology (84-100%). When solid organ injuries were present, specificity declined substantially for foundation models (50-51 percentage points) compared with smaller reductions of 12-41 percentage points for task-specific models. Conclusion: Foundation models matched task-specific discrimination without task-specific training, but their specificity deficits were driven primarily by confounding negative-class heterogeneity rather than prevalence alone. Susceptibility to negative-class heterogeneity decreased progressively with labelled training, suggesting adaptation is required before clinical implementation.