Brian,
If your SME is a domain PDC, read up on the secrets.tdb file.....basically, I have found you must copy the original secrets.tdb to the location samba 2.2.8 stores it...if you don't, your Windows clients loose contact with the domain. My experience is from upgrading SME from 5.5 to 5.6 and 5.6 to 6.01.
ryan