You can't think of anything environmental that might trigger this behavior? Is anyone entering the room, any kind of lighting in the room changing/flickering, any loose bugs in the enclosure? I know you worked a lot on the husbandry before you got him, but have you also been monitoring temps and humidities to make sure things are good (to avoid getting sick)? How does the bottom of the enclosure look (cleanliness)? The 3 times you've seen him do this weird behavior have all been in the past 2 weeks, right? maybe something has changed without you noticing? Just trying to help you brain storm some ideas here, haha.
Oh also, are there any mirrors or other reflective surfaces in the room he's housed in? It's possible he can see himself somewhere in a reflection and thinks its another chameleon and he's being territorial, especially based on your description of the behavior.