Having used a vanilla pfsense box with seperate ADSL connection (draytek vigor 110 supplying pppoe), I continued to have exactly the same problem.
so no multiwan, or traffic balancing, or transparent proxy server issues (i'd spent a lot of time trying to troubleshoot this by scaling back the features i wanted to use).
Incidentally the tech in the government department who supply the test did say that they had problems with ISPs who used transparent proxies.
The solution was to use IPCOP instead - unfortunately i was completely unable to get this working with pfsense but a vanilla ipcop installation did the job fine. Which was nice in one way since i've been using ipcop for a good 5 years and found it to be excellent.
I will continue to use pfsense, as i consider it superior in many ways, in terms of the packages and reporting, and clearly it is actively being developed whereas ipcop seems to be taking a rest at the moment. But i can't use it as my sole solution, at least where these government tests are concerned.