This sounds exactly like the problem which haunted me almost a year ago. See here:
http://forum.pfsense.org/index.php/topic,5909.0.html
I was just looking through the forum if the problem is still there before trying to upgrade to 1.2. Since my solution at the time being was patching pfSense and the patches by now probably have to be rethought/rewritten an upgrade for me is not so easy possible.
However, it's interesting to see that this problem still occurs not only in my setup and it does not seem to have a solution… (I suspect some kind of load-balancing code inside freebsd which "turns" the interfaces in brideged mode, but thats just guessing)
BTW, pfSense is a great piece of work - after patching this problem away last year it runs and serves absolutely reliable. Great work guys.
Best regards,
Arno