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Welcome to the forum! Sounds like you have done some good research on your enclosure, which is great. It may also help if you could get a couple pictures of your set up so that we can see it in action. That will give us an idea of how your lights are mounted and other possible issues.

My first thought, as your temperatures all seem good, is that it simply may be that it is being handled too much for a new lizard. They usually take a bit of time to settle in and with frequent handling this can make the issue take longer to resolve than normal. At three weeks it should have acclimated by now, but some take longer than others.

Do you have a reptile specialist vet in your area? Its always good with a new animal to go get a quick checkup with a reptile vet. That way you dont have to worry so much about past care and the present state of the animal.
 

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Looks like a very nice enclosure, lots of room and youve made use of varying horizontal aspects too. Just one suggestion I would make really, that being to move the fluorescent tube so that it is located all the way over to the right, next to the basking light. Youre dragon in the wild gets both heat and UV together with their visible light, so that you want to have them getting a good dose of all of that when they bask too. You also want to make sure there is an area to the left of your enclosure where there is no UV exposure so that they have a way of escaping it should they need to.

Its not too surprising that your dragon chose the branch to hang out on most of the time. They will usually pick a higher position to hang out on when available. I think it makes them feel safer as they have the ability to survey a larger area.

Aside from that, I would say leave him be for a week or so without holding or messing with him. A week without baths wont be a big deal, and will allow you to see if that is the issue or if its something else. Again, if you can find a good reptile vet then that is also a good idea.

As you have been, make sure the veggies are in there at all times with him. That way if he really needs it, he has food there when you arent. Looks like you might want to try a bit more variety as well. Make sure they are cut up nice and small for the little one. That also ensures you wont have any problems with any crickets you might not find after feeding.
 

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I would have to disagree with that. Probes are not meant to show you what temp your dragon likes. They are there to monitor the extremes of your temperature gradient. Therefore you want one on your basking area (showing hottest temp) and one at the bottom of the cool side (showing coolest temp). The dragon will decide where it wants to go within that range. All other temps are somewhere in between and largely inconsequential, for a new keeper especially. If you want to know what temp your dragon likes best, a simple piece of kit called an infrared temp gun (about 15 quid) will show you instantly with a lazer pointer.

As for the humidity, it will be unlikely that the position of the small water bowl will increase overall humidity and there is no evidence that slight increases in humidity cause any health issues anyway.
 
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