Just looked into it on the BTC Guild side. I've upgraded the bitcoind, but it looks like PoolServerJ's internal workmaker is the problem (Bitlc also uses PoolServerJ). It's making its own work and not including /P2SH/. I'll have to get in touch with shadders to find out how to make it carry forward (I'm not the best with Java).
getmemorypool now returns a field
"coinbaseflags" : "062f503253482f",
which is data that can just be stuck on the end of the coinbase. P2Pool uses it, poolserverj should too.