It sounds that somehow your "Sent" folder in Aquamail got mapped (is pointing to) a different folder on the server.
Go to "manage folders" and check which folder "Sent" is synced with. Please, read the FAQ item "How do I access server side folders?"
http://www.aqua-mail.com/?page_id=227 for the instructions on how to do that.
Also, using Gmail's web interface, do a search for the message you described, to determine which label it has (i.e. in which folder it would appear)
If my guess is correct, then you can configure the correct server-side "Sent" folder (it might be called "Sent Mail" or whatever, depending on your Gmail profile language...