Given the wealth of supplied information, I'd throw a dart at the use of RIP between the two. Check the Novell server and make sure that RIPII is diabled, or at least only listening. MS Winderz don't do RIP II. So, the Novell box should only be blabbing RIP I, and listening for RIP I and II (or only RIP I). There might be a "compatibility mode," for RIP II I don't remember
This may screw you up if you're using Variable Length Subnet Masking (VLSM), and (if that's the case) you may have to reconfigure one/some/all of your routers to make the acommodation.
What may be happening is whatever address you have subnetted is being passed through a RIP I - only segment (which will reset the mask to the default for the address class you're using), and comes out to the next segment as two chunks of the same network (the two subnets are now two seperate chunks of the same network) and/or The Winderz box is getting RIP II information only, and doesn't understand the subnetting (like maybe you have two or more NICs in this server?)
I'm not sure about how Windows handles RIP II, how it sees it, or what it does with it...but like I said, with the given information, that's my first best guess.
My second best guess (supplied by one of the guys I work with) is that perhaps there are address assignments being issued by DHCP that are overlapping with hard-coded addresses (like maybe you forgot to exclude them from the DHCP pool). For example, you have a router at 172.16.1.254/24...and you have a DHCP address pool scoped for 172.16.1.(1-254)...when DHCP issues the ".254" address... the conflict pops up. The fact that there's Novell and MS on the same net is just a Red Herring.
SO, there ya go.
FWIW /.02
Scott