Soft tissue artifacts during motion capture can lead to errors in kinematics and incorrect estimation of joint angles and segment motion. The aim of this study was to evaluate the effect of shank segment axial rotation and knee rotator muscle bounds on predicted muscle and joint forces in a musculoskeletal model of the lower limb. A maximal height jump for ten subjects was analysed using the original motion data and then modified for different levels of internal and external rotation, and with the upper force bound doubled for five muscles. Both externally rotating the shank and doubling the muscle bounds increased the ability of the model to find a solution in regions of high loading. Muscle force levels in popliteus and tensor fascia latae showed statistically significant differences, but less so in plantaris, sartorius or gracilis. The shear and patellofemoral joint forces were found to be significantly affected by axial rotation during specific phases of the motion and were dependent on the amount of rotation. Fewer differences were observed when doubling the muscle bounds, except for the patellofemoral force and plantaris and sartorius muscle force, which were significantly increased in many of the jump phases. These results give an insight into the behaviour of the model and give an indication of the importance of accurate kinematics and subject-specific geometry.