Today it's back. I get the same thing, a large cursor that spins and spins, even when the mail has finished reading. I've tried to isolate it, but can't. It seems to always hang when there is mail, currently, it won't hang when I have no mail (in which case the spinning cursor is small). I've also noticed that sometimes when the cursor hangs, if I exit Aquamail, then re-launch, there is no cursor at all while reading mail.
Sorry I can't be more precise; I will try to narrow it down later today.