Thera, your post didn't include the adjusted code for the light gem, so it looked at first like the compass was inside the gem. Easy fix, though:
[LightGem]
Type=T3LightGemWindow
Placement_X=CENTER
Placement_Y=BOTTOM
Pos_Y=-50
Pos_Z=10
Scale_X=0.5
Scale_Y=0.5
Scale_Z=0.5
Active=VISIBLE
ChildWindow_0=LightGemLight
ChildWindow_2=LightGem_Case
ChildWindow_1=LightGem_Gem
That will keep the gem the same scale as the compass.