That works! I had no idea you had to reset xform after creating a primitive, I just assumed they would not cause any issues since I would not change scale or rotation outside of editable poly. I had a feeling I must have been making a basic error...Thank you so much for your help.
That is what was confusing me, I know that when an object has its scale changed outside of sub-object mode many operations will not work properly. However in my examples I did not scale them, I just created a primitive, converted it to editable poly without making any changes to it and then extruded a few faces and added…