There can be a few reasons for this. Bukkit 1.7.10 was known to duplicate items from time to time.
Are they in the spawnchunks, and does it affect all dimensions?
How often are they duplicating items?
Check to see if all the hoppers are in the same chunk, sometimes that fixes it. Also make sure there's a solid block above every hopper in the clock.
If that doesn't fix it then its probably a rouge plugin.