Thoes holes in the dxf are for countersunk straight holes if you have a plate thicker than 7mm, it says so in the manual. But: I had the same problem but the place cought it and asked me, another user had the problem two days ago where they cut the bigger holes.
@vicious1 You should really think about removing those holes from the dxf, the usual thickness of aluminium is 6mm it seems. Adding countersunk wholes is easier than removing them. 
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