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Z axis not repeating on a vertical machining center

Had a job that I went into today that the customer complained about Z axis varying by 1/16 to 1/8 after a lightening strike. They were running castings and taking mill cuts across the top. This depth seemed to be changing. My immediate thoughts were an encoder problem since that's typicql if the encoder does not read all the pulses.

I began troubleshooting the machine side looking at a few basic things like z axis motor coupling but that was ok. I then decided to figure out if there castings were bad. I checked this by grabbing a height gage and taking it into the machine and measureing the height of the milled surface after it was done machining. What I found was the machine repeated perfectly. Either the parts or how the parts are located on the fixture was the problem. After further troubleshooting determined someone had taken off additional stops from fixture therefore reading off the casting.