Hopper redstone clock duplicating items

When using a hopper redstone clock - two hoppers side-by-side connected to each other with one item placed in one, which moves between the two hoppers every half-second or so and generates a redstone pulse from an out-going comparator - exiting and re-entering a world will sometimes duplicate the item in certain hoppers and then "stick" it to the hopper so that it does not move out of it. Because of this, the redstone pulse stops in these hoppers because instead of the hoppers changing from empty to not-empty, they change from having quantity A of an item to having quantity B. In the first picture I show the mechanism - note how the left-hand side redstone is on but the right-hand side is off. Then in the next picture the left redstone is still on but the right side is now on; the item window in the middle shows the left hopper, which switches between 1-2 buttons, while the right hopper switches between 0-1 buttons, thus producing the pulse, while the left hopper's output is constantly on.