jjenks2006,
I believe that your issue may be that Mozaik is creating a layered DXF with all the components already nested. What the Thermwood Control Nesting is looking for are the individual DXF files for each part. It then uses the OUTLINE layer to nest each part and it's other associated operations into the sheet.
Since you are loading a DXF with multiple OUTLINE layers, it is probably grabbing the first one, using it to nest and the others are being "dragged along" for the ride. Since they are not being considered in the optimization, the geometry/operations for the other parts are ending up off the sheet.
That is my guess.
Contact the Mozaik people and see if you can export/save the parts/operations as individual DXF files.
Brad