Well I don't have a female Gecko but my female rat does this exact same thing. I clean her cage and the male rats cage and usually move things around a bit or add a new item just to keep them interested......the males, being males, check things out and then usually just go eat and curl up in their box, content with life (probably just happy someone cleans up after them like most male creatures *cough cough*) Cookie the girl rat on the other hand "re-organizes" everything and 15 minutes after I've just done her cage it looks like a total disaster area.
I think it's a girl thang! LOL