Hi Danny, it seems they are at some teeny tiny little difference in elevation from one another. Maybe just in one little segment or something, I haven't been able to visually see where the deviation is but if you go to the Front view and grab the corner of the edit frame and bring it down you will get a "flat" snap which won't happen unless there is something to flatten...

Anyway after doing the flattening from the elevation side view, the extrude will then behave how you were expecting, I've attached an updated file here.

- Michael