Yeah, that's becoming annoying. I lose about 30 BTC every time due to the prepay perk. I have now increased connectivity to the bitcoin network to help reduce orphans.

Anyone running bitcoin-qt/bitcoind from bitcoin.org, please upgrade to v0.6.3. It has faster block propagation which helps reduce orphans for all pools.

On a side note, roll-ntime is now enabled on the server for all miners that support it, to increase efficiency. This means your miner program won't need to talk to the server quite as often.