I am so sorry for your loss. What a horrible thing to wake up to.
I suspect the reason your ducks got it but not your chickens has to do with their differing sleep habits. Ducks like to sleep along the "wall" (edges of the cage) at ground level, which makes them very vulnerable to predators who like to reach through. Chickens like to roost up higher, and will tend to sleep toward the center rather than against the edge, so they're less vulnerable unless the only roosts available are close to the edge.
My first thought, like many others, was raccoon, because I've had those losses too, and they sound just like what you had. However, I suspect mink or weasel will do similar damage and can get in through smaller cracks. Whatever you saw doesn't really sound like a raccoon either--they have an almost waddling amble that is quite distinctive, whereas a weasel or mink will have a faster, darting motion. However, until you catch something there's really no way to know.
Hardware wire is one good option to prevent the reaching-through predation, as has already been mentioned. You can also try providing a double barrier--to prevent raccoons grabbing quail feet through the hardware mesh (which they will do, and then drag the whole leg through and eat it off--bloody death), we put a second layer of chicken wire about four inches outside the hardware mesh. The raccoons could reach through the chicken wire, but it limits their flexibility and prevents them doing it quickly enough to catch the quail off guard. I've also placed duckling pens inside of large dog crates, so raccoons can't reach far enough inside to nab the babies.
Another option is electric wire around the outside perimeter to discourage predators from even trying to get inside--you could do that around the garage, perhaps.
Anyway, good luck, and don't give up. It took me many iterations to finally get a system that truly keeps predators out. And I still have to monitor the perimeter regularly and check for weakness. Don't give up, and don't beat yourself up!
