Model VS Live

I have a part that has a surface that is 120 mm long 8mm wide and 1 mm thick with a dozen 3mm holes in it. When I use the cad model to make the program using a 3 point two hole iteritive alignment things are all over the place. The points are in line with each other, and the holes are in line with each other. The two features ,holes and points, are a couple of hundred mm away from each other. I tried creating a plane line and point alignment and the three points were roughly in line nice and nice ready to be put in some coordinate system but the holes and the line are still about 200 mm off location, X 50mm, Y and 12 mm off location in Z.

When I go totally live and use just the part forgetting the model all the points are in the right general area the holes line up where they should be before and after the alignment. Has any one else experienced this with CMM-Ve.

It looks like I am going to have to write this without the benefit of the cad model just curious if any one else has had this issue.

Demon Version 2011.mr1 Global 9.15.8 Win 7. SMA expired about 5 months ago so no help from Tech Sup. Though I do believe they are in the process of renewing it.

I am new to CMM-Ve but have used PCDMIS for 13 yrs. I did attend training at Hexagon in RI last year but had not needed the camera till now. The training for the CMM-Ve was lame at best, most of the class was on the Optiv system and that is a lot different from adding a camera to your TTP system. Trying to convince my boss to give me 2 days one on one at Hexagon to better understand the camera.

Thanks for looking and may you have a great day. Big weekend coming up
Lee