Issues with sustained traffic with PFSense

Last week we had to replace our PFSense firewall because it had a catastrophic hardware failure. All but one of the NICs were taken out of the old server and put into the new one. The one NIC that was not moved was the LAN NIC as this is on-board. The other NICs are all WAN connections and the must all be present (i.e. I can't disable one just for the sake of testing)

After re-installing PFSense and restoring our backup of the configuration, everything came back online just fine, however on the new hardware any download that takes longer than about 10 seconds just times out in the middle.

Example 1: Downloading from Microsoft.com goes at about 900k/sec and times out after about 10 seconds (thus, just under 10Mb of content)

Example 2: Downloading from cnet.com goes at about 300k/sec and times out after about 10 seconds (thus, about 3Mb of content).

By times out, I mean that the download just stops, and you have to pause/resume to get the next part done, repeat and rinse until the download is complete.

However it's not consistant, sometimes it's 10 seconds, sometimes it's 4 seconds, and it sometimes you can't even load a heavy HTML page because the page never finishes.

I assume this is most likely because PFSense does not like the onboard NIC, as this is the primary difference between the two servers. It's recognised as NFE0, and there's no room in the server for any more NICs and I don't have any dual-port NICs handy to experiment with a different LAN connection.

I've never had to troubleshoot this sort of issue before. Can anyone give me some pointers about where to start? BSD/*nix is not my forte so please be kind!

update

As per Josh's suggestion, I tried downloading a 500Mb file using links on the box itself, and it failed after 20 seconds (and 5.7Mb).