I have four Intel PCI Pro 10/100 cards and they are installed on Dell OptiPlex with FreeBSD as OS.
I can see four "fxp?" interfaces. When I connect them to a switch, they are showed as "active". But only two of them are actually working (passing traffic). Another two are not working properly; I can ping them (after I configured IP addresses for them) but I can't ping any other machines on their own lan seqmenets, ie, I can't see beyond themselve.
This is quite possibly a software configuration issue and you might find that you get a quicker answer if you moved this over to the Linux forum (although I do know some of that crew hang out round here too).
In the spirit of a hardware issue though I would swap the cards with those from the working subnets and rule it out. You could also try taking a card you know works and testing each subnet individualy. If each works independantly then it might indeed be a conflict.