If you asked AquaMail to track SSL cert changes, it's going to do exactly that.
There is nothing "magical" about Gmail certs, they're tracked like any other server's, and when they change, the app stops and notifies you about it, just as it's supposed to.
There is one "fine" point here -- since Google can't manage to update the certs on all the load-balanced IMAP servers at once (rolling out the new logo seems to be going better) -- you may get this error multiple times, if you accept the "new" cert and then, due to load-balancing, the app hits a server with the "old" cert.
This too counts as a change, and it is, the cert is going to be different.
One the entire IMAP "server farm" is updated to the new cert, and you've accepted this cert, the errors will stop.