Yes snakes remember negative interactions as well as positive. If you handled yours primarily to give it the betadine bath then it's no wonder he's running and musking.
Fortunately this is easily fixed. I would put him in a small pillowcase, sit down, and put him on my lap. The pillowcase will make him feel like he has a hide and is safe, but while he is in there he will be smelling you and feeling you move around. He may stick his head out to look around, which would be great. You can also put a hand in front of the pillow case opening so he can smell you while feeling hidden and secure (just make sure your hand doesn't smell like rodent!). Eventually he will learn you are not a threat.
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