It's a problem in some games with SLI (and all games with Crossfire). Neither multi-GPU solution works with it perfectly - many people actually report worse performance with SLI enabled when using borderless windowed. Both GPUs are running full tilt, but the performance numbers are way down. It doesn't always effect everyone, and not always in all games with SLI, but it's a known issue. Crossfire just doesn't work in borderless windowed. At all.
As to borderless windowed being more stable - perhaps 4 or 5 years ago, but I haven't had a modern game give me alt-tab issues in fullscreen in at least that long.
Either way, both GPU companies recommend exclusive fullscreen for multi-GPU setups, and many people report a performance and stability differential between the two options. As with any cobbled together hack like SLI/Crossfire, YMMV.
Also, if you move to SLI or Crossfire again, I think you'd be amazed at the improvement - the era of the 500 series was still ironing out some of the big kinks in the technology. Now, games are usually pretty flawless (in fullscreen
) within one driver update or patch after release. Now that a much larger percentage of gamers have multi-GPU, they actually bother to properly support it in games. Except for John Carmack. But he's a bit eccentric.