I've been running Debian (Debian GNU/Linux 5.0 2.6.26-2-686) on MS Hyper-V for over a year now without any clock issues. In the past few weeks I've started seeing serious clock drift on the Linux guests (1s per min). I've not been able to isolate the root cause for the drift and based upon other people's experience with Host/Guest clocks I'm surprised I hadn't had problems earlier.

In testing, I have a base Debian image which does not see the drift. If I install the adjtimex package the drift begins and there doesn't seem to be any way to fix it (removing adjtimex doesn't help, rebooting with notsc or clock=pit doesn't help).

Has anyone seen similar issues and found a resolution?

Not sure about hyper-V, but for VMware systems the following info is useful - perhaps you can get something useful that will apply.

(I suspect that using as recent a kernel as possible might help.)

http://www.vmware.com/pdf/vmware_timekeeping.pdf .
http://kb.vmware.com/kb/1006427 "Timekeeping best practices for Linux guests"

It looks like the resolution is to not install adjtimex. I purged it and all is working well again.