Ok, I made some progress today with Kenny's method, I am able to get thru the first and second tool change and they worked fine. The third tool is the shortest of the 5 used for this part, and it has an offset of -.97". The machine hit the z up limit when doing cycle start for that tool change, which is weird because if that was going to happen I would have expected it with tools longer not shorter, than the reference tool. As an experiment I started over and put in an offset of -.56 for that tool and it worked, running thru the program above the height it's supposed to be at by .41" as expected. The rest of the tool changes, with longer tools, worked fine. So I've narrowed down the problem but I'm still not sure whats causing it, any ideas?