When you upgrade to net-fs/samba-3.4.6, you need to ensure the users will still be able to authenticate against samba. There are various ways to do that, but the simplest one is to add the line below to /etc/samba/smb.conf:
passdb backend = smbpasswd
Of course this is not the best long-term solution (refer to the upstream docs for possible options). However, if you just upgraded, and are wondering why things broke, this line can save you within seconds.