Steps to recreate:

1) Place a chest, point a hopper at it, then point a hopper at that hopper.
2) Power both hoppers
3) Fill both hoppers completely
4) Unpower the hopper farthest from the chest, then the hopper closest to the chest
5) No items flow
6) Remove a stack of items from the hopper nearest the chest
7) Items start to flow both into the chest from the middle hopper, and into the middle hopper from the end hopper

Further situation that may help debug:
1) Recreate as above (1-5), but fill both hoppers with the same item
2) Remove a stack of items from the hopper nearest the chest
3) Items start to flow both into the chest and the middle hopper, but the item count in the end hopper is going down by 2 at a time, so it appears that it is feeding into both. Once the middle hopper fills up again the item flow stops once more