@mandapandabear
That sounds so much like what the Runner babies and I went through!!! Thanks to some loving, kind BYC Duck Forum people (you know who you are), I figured it out.
First, it helps to decide that you're in it for the long haul. It does sort itself out - at least, it did for me, and has for many people.
What you've been told about them being fearful of large critters coming at them from above is true in my experience. And I had the same issue - it was like a scene from a horror movie when I tried to come into the walk-in brooder to pick them up to take them to the tub, or clean the brooder. Mercy. And it happened overnight. One day, I could clean the brooder with them in it, the next day, it was screaming and mayhem.
Whew. Flashback.
So, I got creative. The brooder was in our spare room. Took up the entire room, just about. So I blocked off a section of the hallway, put down an old sheet to protect the floor, opened the door of the brooder and let them "escape" into the hallway while I tidied up. At first they huddled in the hallway. After a few days, though, they felt less threatened and started following me around - at a distance. Eventually, they were following me up and down the hallway (to the bathroom where I rinsed and refilled the waterer) and even to the brooder.
After room service was done, I'd grab a bowl of thawed peas, sit in the hallway, and toss a few peas at a time toward the flock. I'd place the peas closer and closer to myself. The more bold ducklings would actually crawl over me to get to the peas, and as long as I kept my hands to myself, all was well.
Providing a carrier that they can walk into on their own made another huge difference.*
Fast forward a couple of months....the ducks once again were friendly, and have been ever since. If I go out and dig holes so they can get at worms, I literally have ducks leaning against me, standing on me, shoving me out of their way. A few of my ducks like pets and hugs - no one likes being picked up, but they don't panic, either.
Hugs. - Oh, and please join us on the Duck Forum (c:
* I wanted to add this note to anyone reading... that carrier they can walk into has made a HUGE difference in handling skittery adopted ducks. It keeps them much more calm. It is easier to pick them up, too, for vet exams if they are already in the carrier. Ours is a large dog crate that I covered with one inch diameter gap plastic poultry fence (the nightmare was a duck sticking her neck out in transit and having it broken. That has not happened, because we covered the "Limousine" before carrying duckies). I cannot emphasize this enough - having a nice sized crate they can stand up in fully (with Runners this can be an initial challenge), that can accommodate a food and a water bowl, that is easily cleaned, and where I can toss peas to entice them to enter (I do not need to do this, they'd rather go into the Limousine than have me too close), makes managing nervous ducks so much easier.