What sort of time management system do you use

To verify your theory (which, by the way, is sound), execute the following as root:

hwclock --show

This will show you your hardware clock on the server you are executing the command.

To synchronise your hardware clock with your system-time (which is managed by ntp), run the following command:

hwclock --systohc --utc

The last argument (--utc) tells hwclock to store the time in hardware clock in coordinated universal time.

Additionally, please keep in mind that man page for dmesg(1) say the following, so the behaviour you are experiencing is documented and valid:

   -T, --ctime
          Print human-readable timestamps.

          Be aware that the timestamp could be inaccurate!  The time
          source used for the logs is not updated after system
          SUSPEND/RESUME.

You clearly need a more accurate time source for this server.

Since you can't use the internet on this system, your only real option is to install a (or use an existing) time source on the local network. You can set your server to sync from another server on your LAN, which either keeps good time itself, or is synced up to a good time source.

For Server 2008, the instructions on how to configure your NTP settings are here, at KB 816042. Specifically how depends on what type of time source you're using, so I'll leave that up to you to decide, but that link shows you how to do it, and even offers the automatic "fix it" options (though, I personally wouldn't use those on a production server).