It's true that latency can have a small effect on block mining rewards (higher probability of orphaned), but should not impact the number of transactions that are known to the mining node (except for those that arrive in the last moment before a block is found), so it cannot explain these low numbers.
I agree. We're seeing a 40% difference in the number of transactions included per block. Unless the Great Firewall is picking out transactions, I don't see how this is possible. One explanation is that ASICMiner has a custom filter to decide which transactions to include.