Do you have an Atomic Clock in your network?

First, I assume you're talking about buying a GPS time server (perhaps with a rubidium backup) or a GPS clock source that you can connect to your computer, as actual atomic clock is something you probably can't afford unless you work for NIST or the US Naval Observatory.

With that said, if you are dealing with OS compatibility issues, there's no guarantee that a dedicated time server or in-house clock source is going to resolve your issue. Can you share with us some information about your current NTP configuration and heirarchy, and the issues you are trying to solve? It's likely there's a relatively easy solution that doesn't involve spending money on hardware (and cabling; you would need to get the receiver antenna to the roof).

Sorry yes, should have been specific, GPS clock source, functioning as stratum 2 in the network. 

I'm not really trying to fix any 1 specific problem.  Its just problems over time with various systems.  Right now today there is a Cisco core switch in our network that sync's with 3 targets on the internet, then everything in the environment, however many steps removed, sync with that source.  Sometimes we have problems with Cisco switches syncing with that core switch which have been tracked down to IOS version issues, sometimes certain windows operating systems have had problem because of specific patches, we even have seen VMWare specific issues an SAN specific issues.

So fixing a specific issue isn't really at the core of this, I'm trying to build a more stable network time environment.  It was even recently suggested by Cisco directly that we incorporate a GPS sourced atomic clock as part of a Nexus purchase.  My ultimate plan is to purchase 2 or 3 GPS clocks and have them function as primary, then use internet targets as alternates.

basically something like this: Masterclock.com | NTP Time Server with GPS and High Stability

Sorry yes, should have been specific, GPS clock source, functioning as stratum 2 in the network. 

I'm not really trying to fix any 1 specific problem.  Its just problems over time with various systems.  Right now today there is a Cisco core switch in our network that sync's with 3 targets on the internet, then everything in the environment, however many steps removed, sync with that source.  Sometimes we have problems with Cisco switches syncing with that core switch which have been tracked down to IOS version issues, sometimes certain windows operating systems have had problem because of specific patches, we even have seen VMWare specific issues an SAN specific issues.

So fixing a specific issue isn't really at the core of this, I'm trying to build a more stable network time environment.  It was even recently suggested by Cisco directly that we incorporate a GPS sourced atomic clock as part of a Nexus purchase.  My ultimate plan is to purchase 2 or 3 GPS clocks and have them function as primary, then use internet targets as alternates.

basically something like this: Masterclock.com | NTP Time Server with GPS and High Stability