Stepper issue?

[Helicoptermike]

Hello,
I am new to CNC Plasma and CNC in general. I am trying to dial in my plasma set up which I purchased from Viper Plasma a while ago. Overseas work has kept me from getting it up and running and I finally got around to building a table and putting it all together. The first items I cut were a 2 inch disc and a 2 inch square to see how it cut, table squareness etc. Everything went well and I was happy with the cuts. Next I tried a small shape approximately 4 inch x 2 inch that had two interior cuts. I had positioned the torch by jogging to a location, set zero on the dro and cut the shape. What I found was that the interior cuts, which were cut first, were not in the correct position on the part. To check this, I moved the torch to the forward left position, what would be machine coordinate zero, set both machine coordinate and offset readouts to zero, put some tape along each axis as a quick reference and jogged away from this position. I then jogged back to zero and everything looked good. I then jogged away from zero, on all three axis' and used the "Go To Zero" button. This did not take anything back to zero and although the dro read zero on both the machine coordinate and offsets readouts the positions were as much as 3 inches from where I had placed the reference tape. Trying this a number of times gave a different result each time.
I ran the stepper program on the settings page and followed the information I had (a you tube video) on that procedure.
I do not have limit switches installed at this time and although I have a THC but have not wired it in yet. Figured I should get everything working correctly before I add anything else.
Any ideas on what might be causing this?

Thanks for any help and/or information any of you might have on this subject! I really appreciate any info. I really want to get my machine up and running accurately!

Mike