The custom filter is a good explanation. It's the only one I can think of actually. Great firewall appart...

Friedcat already said that they don't do anything special filtering transactions...
We are using the same transaction policy of the official Bitcoin client's default behavior.
Friedcat would agree that 40% of difference on average cannot be considered just statistical noise. There must be a technical explanation, either explicit policies or implicitly as consequences of some technical facts.