I know this is an old post, but I thought I should share my experience. I am cutting 1.25" plate with my CNC plasma. The plate is very heavy, so I bring the plate into the table with our forklift. The plate is never square with the machine axis so I have been rotating the local system after measuring the angle that the plate sits. Making straight cuts using MDI works great with the compensated axis.
Last evening I cut a more complex part posted by Sheetcam. It is hot here in Iowa, about 90F, and when cutting thick plate the plasma needs a break about every 30 inches. I do this through feed hold and toggle the torch manually. This worked fine for three feed holds. After starting the machine after the forth hold, the axis got confused, started cutting along the machine axis. The plate was only off by a few degrees, so it was hard to notice there was an issue, more noticeably, the axis readouts stopped responding.......I had to stop the machine with an E-stop and now I have an 80 pound bad part.
I am going to have to go back to squaring the plate manually. If anyone has any insight, I would greatly appreciate it. Thanks.