Are you sure you are definately using PIxhawk 1, instead of pixracer or something else?
The pixhawk 1 and 2 have the same flash space, so that error shouldn't pop up if your using Pixhawk 1.
Pixhawk1 does use v2, and PIxhawk 2 uses v3.
Also, what branch are you using?
I typically switch to 'stable' to do anything with it (just in case master is not stable).