Just a thought, you aren't feeding near the time you are handling are you? We've had young geckos that began to associate handling with being fed and then would confuse hands with food. For us, we have to turn on the room light to do either, so we turn it on, handle them, turn the light off, leave the room for a while, come back, turn the light on and feed. Then they don't think light on means food or that handling means when I go back into the enclosure there is food there.
Make sure it has plenty of hides too... sometimes they may feel too exposed and that can cause aggression, especially if you pick up the only hide to chase them out to handle them, they need to feel safe somewhere.
Just some random thoughts. Careful handling and time should settle him down.
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0.1 Albino Leo Gecko
0.1 Crested Gecko
1.0 Dear Boyfriend
Departed: Harvey and Spock