Thanks Lee,
The 200Mb was the combined traffic of both in and out, so definitely not scraping the limits of the gigabit NIC's. There also wasn't a vast amount of traffic (from the other product, there were only maximum 4000 packets per second passing through the trunk reported).
I had already used a more powerful machine (Intel Xeon based), and also used Intel Server grade gigabit NIC's too (both equal versions and models), so most of the testing seems to point to enabling M0n0wall's Traffic Shaper being the bottleneck or issue in this particular case.
As for isolating the VLAN's, the switches were also configured with each port configured for a given VLAN (there were no ports with multiple VLAN access assigned), with the exception of two ports for trunking between the switches, which for our required network and infrastructure simulation cannot be changed at this moment. It may be something in the future to test, but for now it appears that M0n0wall can't be used in our current VLAN environments without any significant investment of time for testing.
Which to be honest, the other product seemed to work well and will probably become the "norm" for our future WAN simulations.
But thank you for your comments and information for this issue and maybe M0n0wall may be able to return as a good "all rounder" going forward
Cheers
John