He's just sat with his mate, they had to be seperated from the rest because they were bullying the female and my disabled ducky. Hes not doing anything else out of the ordinary, just making this weird sound.
One of mine (a drake) makes a weird sound similar to the one you described, with a bit of whistling in it for good measure
it's really odd, he's not sneezing or anything, it's just a bit of a funny noise... i don't think it means anything (bad) though. He does it when he's sitting down, standing up, at the water etc... not all the time, but in the half hour I'm out with them changing food and water and things he's usually done it once or twice! He sort of stretches his neck and makes the noise, then brings it down again for the whistling bit!
I've found that my runner girls have quite a vocabulary. It's not all "quack quack."
They have different sounds they make when they're looking for me, when they are frustrated, when they see something they want, when they are content, when they are just staying in touch with each other as they forage in the garden, when they are frightened, and so on.
So I'd guess your guy is expressing some dissatisfaction, based on the circumstances.
My Appleyard ducks make a rapid clicking noise when they disagree with me about anything. Like time for bed. They want to argue about it. So far, the drakes haven't. I tell them time for bed and they just get up and go into their night run.
The ducks form a committee, bob their heads up and down, and want to stand there and discuss it. I practically have to reach down and shove them to get them to move. My son has dubbed them The Ladies' Sewing Circle.