I had to read that several times; hopefully I figured it out!
When you place your ruler on the sewn seam, are you cutting from one corner to the other corner? In other owrds, is the cut from corner to corner? It seems to me the only way you will get unequal results is if the cut is offset from the corner.
Just curious, but what ruler are you using?
Edit: Just realized that you are talking about sewing long strips together. Ignore my comments!