Hi Larry!
My fish get skittish when something unusual happens. Like, when I turn off the waterfall every Sunday morning when I clean the filter and do other maintenance. They will congregate in the deepest end and try to hide. I think that when you turn off your bubbler, this may cause the fish to feel insecure, so they hide, instead of come for food. Try feeding them the same time and place each day, and leave all other factors the same (meaning, leave the bubbler on).
My koi eat like little piggies, but they don't really eat out of my hands. I mean, they will, but it's more like they are going crazy for food, and my hand happens to be in the way. I think that it takes a long time to "tame" them to come to our open hand, and especially to accept your touch. Be patient, be respectful of them, and keep working consistantly at it. You will be rewarded.
They need to feel safe and secure in their home. If mine are frightened or spooked by something, it will take a few days for them to act normally again.
Now think back - everything you do to the pond could be eroding the fish's sense of security. If you just recently netted out goldfish, that could be traumatic to your koi. If you mess with the filter, get in the pond and scoop out debris, any meddling at all, even if it's beneficial meddling, will spook the fish, and that means a few days of them getting to feel comfortable again.
And remember - crystal clear water is not always a sign of a healthy pond. Fish don't mind brown or green water. Have you tested your water quality? Amonia, nitrates, nitrites, pH, salt, etc.? Perhaps the fish are unsettled becasue they are not 100% comfortable in their water's analysis.