The masternodes are working/earning correctly: but as djm34 explained, some of the larger holders, are not paying the masternode fees and instead take 90% of the stake reward for themselves. Masternodes are earning 33% of some stakes, but not earning anything from a bunch of stakes as well.

This problem is twofold, one affecting masternodes, one affecting stakers:
- people running masternodes are not receiving all of their due rewards
- some people are staking with much greater profit than others (almost double)

If this is not a distribution problem, I don't know what is...