Seems to be like you are getting pretty good behavior for what could be a real networking mess.
you have the ISP device coming in and pointing to a hub then the hub connects to one interface on your linux machine and another connectin to a router. Is this diagram accurate?
Code:
ISP
|
Hub
/ \
ETH0 Router
/ | \
ETH1 EQ1 EQ2
My first guess is your router is preforming NAT or something similar (PAT, NAT overload etc). The next thought is that the router is a switch and not a Hub hense the need for the hub in this configuration. This would explain why SEQ never sees data when you filter by MAC address or IP address for your EQ machines.
Still making guesses here. Guessing your ISP provides you with 1 ip address for your home/location. Your router gets assigned that address, which would explain why your SEQ session is confused. This is because it is seeing data that is directed to BOTH EQ machines because as far as the server goes and your ETH0 are concered everythign else either originates from or is going to the router and only knows the router as having it's IP Address and it's unique MAC Address.
It appears to me you are getting the data exactly as your network is configured to allow your SEQ box to get it.
To resolve this issue easily (if session tracking fails) you would need to configure your network into this topology.
Code:
ISP
|
Router
|
Hub
/ | \
/ | \
SEQ EQ1 EQ2
To try and shorten the explination (little late, huh)
Eth0 sees your entire network as having 1 IP address and 1 MAC adress even through there are multiple machines. This is the design of PAT (NAT overload).
Eth1 does not see any EQ packets because your router is a Switch not a Hub.
This would explain the behavior you are experiencing.
Again I guessed at some of the stuff, so if you have other information, like say your router really is hub and not a switch with a false label that says hub... that information would be good to know and would point us possible down a different path.
~ TK