When I make changes to a pattern in pattern mode they disappear after exiting pattern mode

I really think that I'm missing something very obvious here, but I have been trying to figure this out for months and I can't figure out what I'm doing wrong.

I'm trying to make a repeating pattern. I have my shape (just one simple shape with a fill color--no gradient, no stroke, nothing) and I have it repeating about 30 times, in a box (no fill or stroke, about 3"x2.5"). I'm following these steps:

1. select all

2. Object --- Pattern --- Make

3. re-arrange my shapes so that I have a seamless transition/edge on all sides

4. click "okay"

Every single time my shapes get shifted around after I click "okay", leaving me with a not seamless pattern. What am I doing wrong please???!!!