I'm getting the same problem using an IMAP email account, i get the following message when i refresh my inbox:
"Error checking mail: Invalid server response"
I don't recall ever seeing this problem before the latest update of the app.
The problem seems to be related to one particular email in my inbox, if I move this email from my Inbox into another folder using my desktop email client, i can then successfully refresh my Inbox using AquaMail.
I am happy to provide the problem email to help with debugging Aquamail (I tried to post it here but it exceeds the 20000 character limit and this forum doesn't allow links)