That explains maybe why the "generic" rectangle doesn't work. Using my own now and it's perfect. It is that file that comes by default that is the problem.
The BOM is not formatted properly for any full integrator that I have found (manufacture the pcb, supply parts, place parts etc). The placements in the pnp file are missing some orientations etc and the BOM is not in a format that anyone takes that I have found (perhaps some do, I just haven't found any).
For manufacture you need a centroid/XYRS file for pick and place. Now, some places will in-fact process the Gerber files and create the centroid files for you (for a fee).
Here is a really simple example: http://i.screamingcircuits.com/docs/SampleCentroidFile.txt
Most software like KiCad, Eagle, Altium etc all output centroid files to send straight to manufacture. BOMs in CSV or XLS files are often accepted if formatted correctly but then getting that BOM to the actual floor requires the centroid file.
Thank you so much for all the input 