A numerical investigation of an experimental dual-mode scramjet configuration is performed. Both experimental and numerical results indicate significant upstream interaction for this case. Several computational cases are examined: these include the use of jet-to-jet symmetry and entire half-duct modeling. Grid convergence, turbulence modeling, and wall temperature effects are studied in terms of wall pressure predictions and flow-field characteristics. Wall pressure comparisons between CFD and experiment show fair agreement for the jet-to-jet case. However, further computations of the entire half-duct show the development of a large side-wall separation zone extending much further upstream than the separation zone at the duct centerline. This sidewall separation is the dominant feature in the CFD-generated flow field but is not evident in the experimental data, resulting in a unfavorable comparison between CFD and experimental data. Current work aimed at resolving this issue and at further understanding asymmetric flow-structures in dual-mode flow-fields is discussed.