I still haven't identified the root cause of the problem, but I have been able to see a pattern. The payout script is stalling on either ContiniumCoin or Teacoin every Sunday morning. I recently moved these two coins from the old system on to this new platform, hence the sudden issues. I will start expanding the backend part of the platform horizontally (adding more database and payment servers) in the coming days. This should relieve some stress on the one database and payment server currently being used to handle almost 40 pools.
For now, I have manually kicked off the peercoin payments.