I am building a network monitor/analyser in a linux box (Ubuntu server 8). It basically logs ip traffic.

I have installed two network cards, and they are identified by the system
as eth0 and eth2. My problem is I want them to be completely independent of each other - each with its own ip, etcetera. When I
try to do this, it looks like it should work, but the physical cards
respond to each others ip address. This is confusing. I want one
card to be my regular LAN connection, the other to be dedicated
to data collection (promiscuous mode).

Any ideas on why this might be happening, and where I should look to
fix it? Thanks for your attention.

Let me clarify: your problem is that

1. the shortest route between your 2 cards is along the pci bus, and the pc has noticed that.
or
2. card a responds to the ip for card b?
Suggestions
1. Maybe a virtual box for eth2? Maybe another box for eth2?
2. Have you ethernet bridging set up? Are they both logged into the same server? What does your routing table show?