Thanks for all the replies, there wasnt really an issue, it was just slow as the log reader agent was trawling through the log and skipping any tables not marked for replication. See here

http://social.msdn.microsoft.com/Forums/sqlserver/en-US/2c8549dd-a35f-4ccb-8e54-2de45fa06687/transactional-replication-performance-critical-publisher-to-distributor-very-slow