To reproduce:
1. Open attached project
2. Open scene "CalcHeightWrong". It contains a 1st person controller and a cube trigger collider. The scene camera also has a script with an empty OnGUI()
3. Enter play mode and press space - it calls the function GUISkin.label.CalcHeight() and outputs the result in the console (which should be 106)
4. Now walk through the cube - the same function is called but the result is different - 126

Usually just walking through the cube can provide different results. This is somehow related to the empty OnGUI() script attached to the main camera as disabling it makes the GUISkin.label.CalcHeight() return a consistent value.