It seems I read somewhere there is some kind of issue using a windows box as a ntp server . Maybe this might help you track it down.
http://www.cisco.com/en/US/tech/tk648/t ... 3d02.shtmlBasically this is what it says.
Unable to Sync NTP to W32 Based Time ServiceWhen Cisco routers are configured to use the NTP servers placed in the Active Directory, the Cisco routers do not receive any NTP packets
from the NTP server. This issue occurs because Cisco routers use NTP and Active Directory domains use W32Time service. W32Time uses
Simple Network Time Protocol (SNTP), a subset of NTP, for time synchronization. SNTP and NTP use the same network-packet format.
The main difference between SNTP and NTP is that SNTP does not provide the error-check and filtering functions that NTP provides.
Cisco router and switches use NTP and allow for all error-checking and filtering functions provided by NTP v3.
Windows W32Time shows that it is an SNTP implementation inside (rather claiming itself NTP). Cisco IOS-NTP, which tries to sync with W32Time,
gets its own root-dispersion value that it sends to the W32Time and this proves costly for Cisco IOS-NTP to synchronize. Because the root-dispersion
value of Cisco IOS-NTP goes higher than 1000 ms, it unsynchronizes itself (clock-select procedure). Since the Cisco IOS based routers run the full RFC
implementation of NTP they do not sync to an SNTP server. In this case the output of the
show ntp associations detail command shows that the server
is flagged as
insane, invalid. The
root dispersion value is in excess of 1000 ms, which causes the Cisco IOS NTP implementation to reject the association.
Routers that run Cisco IOS can be unable to synchronize to an NTP server if it is a Windows system that runs the W32Time service. If the server
is not synchronized, the routers are not able to transmit to and receive packets from the server.
In order to workaround this issue and sync a Cisco IOS based router, use an authoritative NTP server on the Internet, a UNIX box that runs NTPD
or a GPS on certain platforms. As an alternative, you can choose not to run the W32Time service on the Windows system. Instead, you can use NTP 4.x.
All versions of Windows 2000 and later can serve as an NTP server. Other machines on the network can then use the NTP server to synchronize their time.