What biomechanical model are you using? The devil is in the details…
It's not about how you capture a subject. The problems are related to how you trajectories joint centers.
When capturing data related to human movement everyone will work to track some point on or around the body-- regardless of the technology platform. From those tracked points, we will work to tragectorize a new location inside the human body (ie. identify a hip joint center). This joint center is the root of all biomechanical calculations. From that information you can calculate kinematics and kinetics about a human's movement. Those kinematic and kinetics calculations are fairly standardized in the scientific community, but they have overlooked the model used to trajectories the joint centers. There are a variety of models used for this (Helen Hayes, Cleveland Clinic, etc.), and all of them calculate different joint center locations. Only recently has MRI technology been used to create a ground truth measurement of where joint centers are actually located. The novel research is making some points very clear.
1- If you alter a skeleton model for kinematic or kinetics calculations you will significantly change the outcome measures.
2- There is no standardization for this process.
Therefore, when you are collecting data to make important decisions, make sure you are using the best model for your needs. Because, the more you change or continue to see as indifferent the more you will poorly impact a person's motion health testing repeatability.