Well, ripping everything apart, trying various pci network cards, and putting it back together, allowed me to determine that putting it back exactly how it was fixed my problem. Not sure exactly why (maybe just having the modem unplugged for a while) it is now fixed, but it is.
What I was able to find out, is that the jetway case I bought to go with my intel motherboard is a pain to work with, and I cannot get the pci riser working reliably with the atom motherboard (I can see the network card, but it isn't able to get any traffic flowing through it, and I get a bunch of watchdog errors). But that is a problem for another day ;)