Repeatability in x and y direction during program

OK, I have been having problems running a basic spoil board program. My 1F is not remembering coordinates with the same bit doing different holes on the same job.

I have a program that is putting dog holes and threaded inserts holes in my spoilboard as well as holes in the table itself for the threaded nuts. I ran the part with the threaded holes on the spoil board, everything looked good. The first part of the program drilled down through the 3/4" spoilboard into the table(into table about 1/4"). Removed my spoilboard to drill the holes into the table to install the e-z lok threaded nuts, same bit, changed the z ONLY (kept the same x,y). Then noticed right away that the holes didnt line up. They were off roughly 1/8" or so in both the x and y directions.
I checked the wire connections (looked good), ordered a new set of wires from 1f and no change. There are no grinding or strange noises moving in any directions. Temp in the shop was around 60 deg f. Machine is the original woodworker.

Is the behavior repeatable where you probe Z and it moves the X,Y home position as well?

Repeatable in the way that it is inconsistence. Never the same x,y.

Another weird thing that is does is when typing in g code manually. If I home the machine, I can type in something like (g1 x10 y10) and it will move to that spot in inches. If I try to do the same thing after I zero the machine to the spoilboard, it will move to that spot in mm, even though the 1F interface is setup and displaying inches.