I did some testing and I can see what you're seeing when I use the "GPS Receiver Height" in the GPS Setup box. I'll have the programmers fix this.
However, when I enter a Receiver Height in the Offset box (Config - Logging - Offset), this does work. I verified that the offset was applied to both the .gpl file as wel as the shape file (actually the .dbf). So that should be your work around.