Thanks David, turns out scaling the model to 1 while adjusting markers at the same time was the way to go. Not sure why...

I have been trying to scale a generic full body model in to experimental marker data provided by Dr. BJ Fregley (U. Florida) for a class project. When I only select the "Scale Model" box in the scale tool and make the necessary adjustments (renaming / repositioning markers, etc.), it works fine. But...