What is the CPU utilization? Are there any queues filling up?
The packets are either getting delayed by QoS, or the router is too busy being a proxy to respond to ping, which is low priority.
Depending on the size of your network consider putting in a dedicated proxy, such as Squid.
Thanks again Fewi, at the moment there is very little utilization, I have only one test user running on a RB1200, I've seen a few posts regarding this but no resolution, I don't have any firewall rules or anything, just NAT masquerading and http port 80 redirection to 8080 for my transparent proxy.
Anyone thing else I can try besides installing squid?