What kind of slot does you atom have? If it's PCI, you could probably grab a dual 10/100 Intel card from ebay for about $15. You also might want to see if 2.0 handles the realteks better than 1.2.3.
PCI-e :(
Well it has PCI, but it's not accessible inside the case because of the way it's laid out. It's a Supermicro server. Scalability is also a concern for me, at least with a standalone PC I can upgrade whatever is needed, not the case with an Alix board.
A lot of Realtek problems can be solved by disabling various hardware options which are not well supported. A lot of those options are disabled by default in 2.0.
I had to install 1.2.3 as 2.0 wouldn't boot from the CD, I suspect it didn't like my USB CD drive which I found odd considering 1.2.3 booted and installed without issue. I did however upgrade to 2.0 once I got 1.2.3 installed but the NIC problems persist. I get lots of weird stuff like DHCP timeouts and such. Never could pinpoint the real issue other than these Realtek NIC's just not playing nicely. I disabled the hardware checksum offload etc. and it didn't make much of a difference. Could be the VLAN's acting up as well as that seemed to be where most of my problems were occuring.
Think I might deploy a fresh 2.0 install with a dedicated CD-ROM just to see if my problems persist or go away. If not, then I'm still looking at options, may just end up biting the bullet and getting a dual port card or building a mini-itx system from scratch with Intel NIC's… don't want to really spend any money, but I don't think I have any choice :(