So the Divot in the top of the hoppers causes items to not be pushed across them like vanilla hoppers.
This means that they can't be used for in world changes of item stacks (such as create), or flowing water distribution systems (since the items all catch on the first lip).

Closing since the mod is no longer supported and will be superseded by a new mod for modern Minecraft versions in the near future.

I have rather no idea why vanilla hoppers work and these don't, maybe something with the aquatic update?