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Cad coordinates changing to machine?

I am having trouble writing a simple program, I call in the cad, click on a hole to start, it reads as the cad, I measure the hole and it changes the nominals and vectors to what appears to be machine coordinates. I measured three holes to align to, again, in machine coordinates. I even programmed the three holes, nominals are in cad, aligned the holes, then measured the holes, the program went to machine coordinates? I asked the guy I work with to write a quick alignment on his cmm, measuring the part, and it works? Is there a filter turned on that I do not know about? I rebooted the software, just in case, now I will shut the system down and see if that helps. Thanks in advance.

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