in my experience the deletion (move to deleted is what I use) doesn't happen right away,
as I told you in the past I've got thunderbird open at the same time (sometimes) and
when I've selected messages to delete from within aquamail, they aren't gone instantly,
same thing has happened when I was having the gmail web interface open in the browser,
and since I'm crazy with tidiness, what I do is another refresh (on my inbox) after I delete emails,
because I want them gone!