We are not sure what is going on here. Ultimately I may have to post the config for you to give me an answer. We have a Cisco 4948 and are able to communicate between two networks/two VLANS (172.17.x.x and 192.168.x.x) on our 4948. We do not have inter-VLAN rounting enabled. Is there something simple I should check within the config that would cause this?
Sorry, I was not clear in my earlier post. As soon as you enable routing on the switch (not considering the routing protocol), the switch will include and route between all the subnets it is directly connected to. So, irrespective of whether you have the subnet under EIGRP or not, the routing will still happen (this routing is happening locally). So, only way to control them is to either disable IP routing (no ip routing) or configure access-lists. If you disable routing, I am affraid some of your other services might suffer (you will not be able to send traffic out to internet from these vlans). So, the best solution is to use an access-list on the interface and block the communication.
Hope this helps.