If you specifie the coordinates of an execute command, these are ignored.
So, Let's say:
The Player's current position is at 100 150 200.
A command block runs the following command:
"/execute Player 500 200 -500 spawnpoint Player"
It should be setting the spawnpoint at 500 200 -500, but it's setting it at 100 150 200.
By the way, "/execute Player ~ ~ ~ spawnpoint" does not work at all.