I just got an older 2.1RC0 to assign a 2001: address on both the WAN and the LAN, but ran into another problem: the DHCPv6/RA server for pfSense really doesn't want to run without a static IPv6 address, and the DHCPv6 relay configuration page seems to be missing an option or two. I'll have to tinker with it later...
As for the WAN disappearing, is it an fxp card? IIRC there's a regression in the upstream FreeBSP fxp driver and it likes to make the card go into an infinite loop of bringing the link up, then dropping it, then bringing it up, then dropping it...