Since updating my kernel of my linux server, the 1Gbit card (r8169) gave troubles. Occasionally, the link went down.
dmesg shows some PCI quirks and IRQ routing conflicts but afaik it's been like that before.
Although I also had enabled the onboard USB ports and added USB to the kernel.
I then tried loading back the old kernel version only to find out that the problem persisted.
Could the card have gone bad? Sure it's a coicidence. Or perhaps the driver is just buggy somehow. I will test the card in another PC.
Back with the old and slow r8139, it seems to work just fine.
I hate this kind of crap. It takes too much time to figure out.