it is probably normal as 1000 confirmations are still a good amount of time to reach (I'm mining from 3 days on that pool, but my wallet is still syncronizing to the chain, so I can not know if I get payout already).

Back in time when i run Incakoin pool on multi-pool.info, I execute the payout after 250 confirmations by anticipating the 5000 real confirmations, so users get coin soon  

Unfortunately my pool is not running as old server get disk failure and I had not yet restart the new powerful server for lack free oftime, even if I had the backup of all