MPM UP2000 HiE Z problem

The Z-axis Drive card on our MPM UP2000 HiE fried. We replaced it with a new card, setting all the jumpers to match the old card. After that we had to recalibrate the Z-axis and the snugger height but the problem is that the camera is now too close to the board during vision height. So close that it is scraping the boards. Under the focus meter in maintenance mode, we found the auto-z for the board. We run that and it moves away from the board and displays the old and new value but when we go back out and try to load the board to vision height it is right back to hitting the board. Can anyone recommend any way to fix this or tell us what we are doing wrong. A copy of the Machines calibration procedures would be great as well. Its possible that we aren't doing one of them correctly because we are just following the machine promps when we click on the calibration. Any help would be greatly appreciated.

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