I think one of the reasons for FreeNAS using FreeBSD was the support for ZFS and RAID Z - seemingly invaluable tools for a file server (from my impressions).
Last I dealt with it was about 3 months ago and yes it only seems, to effect certain nics. I saw a few experienced people looking into the problem but it was months and months before I found it and nothing had been solved. Finding anything on it is a royal pain in the you-know-what since the search terms are so generic.