It sounds like you are using the wrong slots for cutting. I like to mark the slots I am cutting with a post-it so I don't cut the wrong one.

Turn the ruler so that the zero is on the right and line up your fold on the black line. Start cutting at the zero to even off, then cut every 2-1/2". When you cut all you can, take the ruler off, move the strips you already cut, move the fabric over if necessary and line up your cut edge on the zero again.