Hi bigseb - surely if Powermill is sensitive to needing surface normals pointing in a particular way it must have some tool in there for flipping them.

For doing it in MoI the Flip command that Mike mentioned has some more details here:
http://moi3d.com/2.0/docs/moi_command_reference10.htm#flip

Also if you make your object into a fully joined solid instead of just an open surface it will then automatically get the surface normals pointing to the outside of the solid volume.

- Michael