Scenario: 3000 masternodes exist, I have 1. After 500 blocks, I get my payment. At this point I wouldn't be eligible for another payment for 2500 blocks. However, I could send the coins to a new address and restart the masternode, and once its confirmed I'm eligible again immediately, this time it takes say 2000 blocks, but after I do the same, new node. And finally a third time I get my payment after 1000 blocks.
Summary: 3500 blocks have been found. I have gotten 3 payments. Ideally, I should have only gotten 1 payment in this time - 3 would require 9000 blocks.
What am I missing?
Dunno if you're missing anything, but maybe you should have to have number_of_masternodes confirmations before you're eligible for payment?
EDIT: You described a scenario which was very lucky for you. With your example numbers, if your node is new, you have 1/3000 chance of getting paid each block. It doesn't mean you're guaranteed to be paid after 3000 blocks at the latest. It could just as well go like this: after 500 blocks, you get your first payment. Then you create a new MN with your 1000 DRK, but this time it will take 10000 blocks to get the first payment.