You have to find the 'sweet spot' in order to move them. It's usually in between two boxes at the top -- you'll know you're there because the cursor will change to include the up-down/left-right repositioning symbol on it.
If that's not working, double check and make sure click-through isn't enabled. If that's enabled (and it can be enabled on the hotbar, not 100% sure) then you'll have to disable it in order to move the window.
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