Magnetic resonance imaging is often used as a source for reconstructing vascular anatomy for the purpose of computational fluid dynamics (CFD) analysis. We recently observed large discrepancies in such "image-based" CFD models of the normal common carotid artery (CCA) derived from contrast enhanced MR angiography (CEMRA), when compared to phase contrast MR imaging (PCMRI) of the same subjects. A novel quantitative comparison of velocity profile shape of N=20 cases revealed an average 25% overestimation of velocities by CFD, attributed to a corresponding underestimation of lumen area in the CEMRA-derived geometries. We hypothesized that this was due to blurring of edges in the images caused by dilution of contrast agent during the relatively long elliptic centric CEMRA acquisitions, and confirmed this with MRI simulations. Rescaling of CFD models to account for the lumen underestimation improved agreement with the velocity levels seen in the corresponding PCMRI images, but discrepancies in velocity profile shape remained, with CFD tending to over-predict velocity profile skewing. CFD simulations incorporating realistic inlet velocity profiles and non-Newtonian rheology had a negligible effect on velocity profile skewing, suggesting a role for other sources of error or modeling assumptions. In summary, our findings suggest that caution should be exercised when using elliptic-centric CEMRA data as a basis for image-based CFD modeling, and emphasize the importance of comparing image-based CFD models against in vivo data whenever possible.