Windows DHCP Clients Randomly Revert To Old DNS Servers

Bravo on deciding to get rid of static IP assignments (except where absolutely necessary). I'd tell you to use the DHCP database as your "IP address list" documentation, too. Put in reservations for devices with static IP addresses assigned, as well. Make the DHCP database be the authoritative "IP address list" instead of having spreadsheets, etc, that fall out of date.

Here's some background re: DNS and DHCP in Windows. It sounds like you may not be aware that the client computer performs half of the registration (the "A" record), and can also perform the "PTR" record registration, too. This allows you to use virtually any DHCP server you want, so long as it hands out addresses of DNS servers that can accept dynamic registrations.

The Windows DHCP server performs backups of the DHCP database to the local hard disk drive periodcially. You can also export the database with "netsh" (W2K3 or newer) such that restore it to another server easily. Restoring an ISC DHCPd scope to another server is a matter of copying the relevant portions of the dhcpd.leases file and the dhcpd.conf file. Embedded DHCP servers may be more problematic in a restore scenario.

As stated above, your Cisco routers can hand out DHCP to Windows PCs, but the PCs can register their own "PTR" and "A" records. Have a look at the Group Policy setting "Register PTR Records" located under "Comptuer Settings", "Administrative Templates", "Network", and "DNS Client". The client will register the "A" record itself by default.

I wouldn't got with a roll-your-own Linux DNS deployment for this application. You're going to put a lot of time in it, and it will always be the source of "Gee, will this work with Windows Server 2029..." type of musings. If not for Active Directory, I might think differently. Since you've got AD in your environment, and since Microsoft tests AD on Microsoft DNS, I'd use Microsoft DNS.

Windows Server does not have the capability to sync DHCP server databases so that you can have multiple authoritative servers for the same subnet. This continues to be decidedly sub-optimal in Windows DHCP. This might be a "win" for ISC DHCPd on Linux. I haven't got any experience with this capability to share a DHCP lease database across multiple DHCP server, but it certainly sounds sweet. I am not aware of any capability in Cisco routers to do this. Again, you can have your PCs register themselves in DNS regardless of what DHCP server you use.

You could rig up active / passive DHCP on multiple Windows Server computers with some scripting and the native database export functionality, as well.

Personally, I'd go for the option of using Windows DNS everywhere, Windows DHCP everywhere where you can have a Windows DHCP server on the same LAN as the clients, and your Cisco routers handing out DHCP everywhere that you can't have a Windows Server computer. The Linux ISC DHCPd solution might be a "win", too, but I'd stick with Windows DNS.

Is your Linux DHCP client asking for dynamic DNS update? I can't see any information in your question about that, and without it your Linux DHCP requests won't get DDNS registration on the server side. Look at the "DYNAMIC DNS" section in dhclient.conf(5) for details of the settings required.