Rick,
If you create a tool path with ArtCam in normal 2d style what you get is a tool path that cuts an XY direction profile. That won't work on the indexer, what you need is a tool path that cuts in an XZ direction profile. Just think of it as cutting a profile on the table and the turning it up on its edge so the Y direction cuts are vertical to the table.
That's why you need to swap Y to Z.