If the model has a built-in portrait, the geoset with the portrait background often causes the HP bar to be too high up, since "calculate extents" considers the top of the portrait background to be the highest point of the model, instead of considering the top of the unit's head as the highest point.
You could try this

Go to to Windows-->Sequence Manager. Open an animation, and lower the Z value in Maximum Extents. Do the same thing for all animations. I'm not sure if this solves the problem, but I guess it's worth a shot.