Well I've seen some funny bugs in my time. Once it was a printer which would take an hour to print in Holland. The cause was hidden during DST, but in winter when they were GMT+1, a UTC v localtime bug surfaced!
Thanks for the appreciation, but I was really firing "hunches" at you, as I know what it's like when these weird stuff goes on and it is crazy but you cannot find answers.
xntp is the NTP implementation that is installed with most Linux distro's, I also use chrony in cases where the machine is irregularly running Linux or does but not connected to the Internet that often.
ntpdate is a command to set, your clock to Network Time. You should find some NTP servers, that are local to you, perhaps your ISP has something like ntp.some.where.net defined, usually they are ntp0, ntp1 or ntp2. The ntp.org pool is OK, but there's regional versions.
If the time is the problem, then actually it'll be the Squid cache server, and the Win Credentials logon server that need to be in agreement.
Rather than configure server to use a Win time service, you set up the Win time server's clock to be set to NTP on boot.
Reading the M$ explanation, I see they use Kerberos, well I did not know that till now, the problem was seen with BIND/Hesiod. Part of well run network IMO is to have automatic time synchronisation, to reduce maintenance, and ease problem tracking through log files, eliminating clock skew.
http://www.ntp.org/ has public timeserver lists, you may need to open up a UDP port in your network firewall.
http://www.pool.ntp.org/zone/north-america http://en.wikipedia.org/wiki/NTP_pool is a nice explanation
Try
ntpdate -q {2,3}.north-america.pool.ntp.org
Which should give you "offsets" from your clock to the servers, but not update your RTC clock. These pool entries are selected at random by DNS round robbin, so it is better in ntp.conf to use a stable ISP NTP server or two, may be a Uni one somewhere that's Stratum 2 or lower, if you're going to run NTP service in your network.
You should know whether your RTC is set to localtime or UTC as is usual on servers.
Synchronising via command, daily or every few hours via cron should be more than accurate though for most needs, I do like to run NTP server in tandem with DNS, for convenience reasons in network. xntpd supports broadcast, so it's possible to have Zeroconf on workstations.