Windows 2008 R2 DHCP server not responding to DHCP discover

You haven't actually verified that the Windows Server machine is receiving the DHCPDISCOVER requests. I'd throw a sniffer on it (either Microsoft Network Monitor or Wireshark) and verify that the packets really are making it to the server computer.

Are you certain your Ethernet switch doesn't have any "fancy" DHCP-related functionality that might be getting in the way? Your disappearing DHCP packets that you describe toward the end of your posting make me wonder if the switch is "swallowing" them somehow.

Edit: Zow-- I'm a moron! Talk about not being able to read.

Here's a silly question: Is the server computer's NIC configured with an IP address inside the subnet that the DHCP scope encompasses? If not, you'll need a DHCP relay agent (which could be running on your router) to forward the request to the server because, even though it's receiving the request at layer 2, if the server doesn't have a NIC in the subnet with the scope (or if the request doesn't come from a relay agent in the subnet that corresponds to the scope) the server won't answer.

If they're just RFC1918 IP addresses, go ahead and edit your question to include the server computer's IP address and the DHCP scope metes and bounds.

This is probably not the best way to solve this problem but it worked. Here's what I did.

1) I added the following restriction to my Debian-based DHCP server and removed all of the fixed-address entries. This forces any clients in those IP ranges to move somewhere into the .41 - .199 range, otherwise when I turn on the Windows Server clients will receive leases with IPs in the .11 - .40 range that are already present on the network. I then let things sit long enough for any leases in that IP range to expire and have a new one issued.

subnet 192.168.61.0 netmask 255.255.255.0 {

        option routers 192.168.61.1;
        option subnet-mask 255.255.255.0;
        option broadcast-address 192.168.61.255;

        pool {
                range 192.168.61.0 192.168.61.40;
                deny all clients;
        }
        pool {
                range 192.168.61.41 192.168.61.199;

        }
}

I could not figure out a way to make the Windows Server DHCP implementation act as "authoritative"; the behavior I wanted is when clients with leases from the old Debian-based DHCP server sent their DHCPINFORM packets to the new Windows Server, I wanted those clients to receive a DHCPNAK and the go through the whole process again to get a lease, thus "re-populating" the addressing space from .11 and up.... regardless, continuing on.

2) I cheated by expanding the Exclusion range on the new Windows DHCP server to include 192.168.61.100 - 192.168.61.199. This will force any clients who were assigned an IP in that range by the Debian-based DHCP serve to have their DHCPINFORM denied and then issued a new lease at the "bottom" of the addressing space (.11 and greater).

3) At this point I simply turned the Debian DHCP server off, and the Windows Server on and let the expiry time sort things out. Because of the "deny all clients" line in my dhcpd.conf, there were no clients with "old leases" in the .11 - .40 addressing space that could cause an IP conflict, and because of the Exclusion of .100 - .199 ranges all DHCPINFORM requests were denied (at least I imagine that's what happened... I didn't bother looking at the transaction using a packet sniffer... I probably should of) and the addressing space was re-populated starting from the lower bound of .11.