Hi Guys
I finally got a resolution to my horrendous webgui speeds and web traffic through my pfsense router. It turns out our WAN was connected to a dodgy piece of Cisco hardware (Line Card) and it was causing all sorts of problems foe specific traffic from Windows machines only! Here is the explanation I got form our provider.
_We believe we have hit a bug with the particular hardware revision that card is. It drops packets of certain sizes which matches up with that we were seeing with duplicate acks and retransmits that looked like they weren't being acknowledged. I am going to have to look further into why Windows appeared to be affect but other operating systems we tested weren't.
The second line card in our colo router is a newer revision which doesn't suffer from the bug._
This report came just before I was about to do a full reinstall of our router thinking there was some major problem with pfsense. Pheeeew bullet dodged.