There is no pnp vs no pnp on either the nvideo motherboard board or the other new motherboard I am testing with, so I cannot tell if the pnp or no pnp setting changes this situation (both are award bios, recent versions). I have upgraded the BIOS to one which lets me separate the interrupts, and that also does not seem to significantly change the issue -- eth0 and eth1 still get confused some what randomly.
However, slots and interrupts do seem to have a relationship, at least in the devices I have been testing, though it is not a fix. I have also tried to tweak the modules load order, also, does not seem to help.
I did have lots of fun with insmod and modprobe as a result, to get things running again, after tweaking these int settings and messing with slots. But that said, the 8139 card(s) just were too weird with Debian testing and the AMD-64 (as well as AMD Semp x386 stuff) I have been using (a 2.12 type kern.).
However, use of a wholly different card, in the case I was testing, a Linksys 10/100 PCI card,
completely addressed the problem, and now no more eth1/eth0 flip-flop. Note that this situation was and is re-producable with two
different new motherboards, running different AMD devices, and different 8139 cards, and even another RTL card, all using PCI (modern 8139too-style) ethernet cards. No ISA (ugg).
Something odd seems to be afoot hear, and me thinks it may relate to pci probing, somehow. It seems to follow (though not perfectly) that it lines up one way on cold boots, and another on warm ones.
It even seemed to do it once during operations (I had a remote ping routine running) which really scared me. But this has not been reproduced.
I have a fix by junking the card, but it still bugs me.