@Jason:
@nuro:
I forgot to mention, the link graph on the cisco shows 1000's of packet errors after 2 or 3 minutes after the port is re-activated.
Are both pfSense systems plugged into the same Cisco switch? If so, are they in the same physical block? Most switches use multiple controllers inside and I've had a couple flake out and either not establish links or experience high packet loss but only in a certain 8- or 16-port block (out of 48 ports).
EDIT: Also, try fixing both the switch and your pfSense boxes to 100 FD if either is set to auto-negotiate. I recently had an issue with a new carrier and not being able to get more than 2Mbit/s upstream. As soon as I changed the ports it spiked up to 20Mbit/s (what I'm paying for).
The two servers are on separate switches, but the nics for each machine are on the same block. I'm going to try your suggestion and shuffle things around a bit, and set the port to 100 FD. Thanks.