Part of the problem is that for the majority of his life, he has been stuck in a little cup. When food was dropped in, it had nowhere to go and there was no one else to eat it. There was no filter current to blow it around.
Try turning off the filter during feeding. This will help him.
Also, because of living in such a small space before you got him, his muscles are weak and he is adjusting to the new current in the water that is produced by a filter, as well as adjusting to the fact that his home is no longer 3 inches tall. He's still trying to figure out how to eat!!