My transparency files work fine for most clothing. For some reason, the female biker shorts seem to leave a residual filmy reflection in areas that should be transparent. I've tried setting the reflection setting to different colors and different numbers. I even tried using the group tool to eliminate sections of the thigh. Nothing seems to be working. Is there a simple solution I'm missing?

You know those areas of the transparency map you painted black to make transparent? Paint the texture map pure black (RGB 0,0,0) in those areas, also. What you're seeing are probably highlights, not reflections. Highlights don't show up against pure black.