This is a direct rip from another site. I have not modified this text by choice and hope the original writer wont mind. I found this because I was watching my pile of bsdpan- ports growing and needing updates and didn't really fancy doing it by using the perl package system.
FreeBSD 9.0 issues with Quota
There is an issue with FreeBSD 9.0-RELEASE and Quota with a UFS2+SoftUpdate. Apparently it doesn't update the quota file as it should.
I found this in the freebsd-stable mail-list archive.