Gmail's POP3 server is very special.
It only "shows" each message to a mail app once, and then never again.
If you really need POP3, please add "recent:" to your login in AquaMail -- as described here:
https://support.google.com/mail/answer/47948?hl=enIn Aqua, long press the account -> account setup -> Manual
You'll be looking at incoming server settings. Just add "recent:" before your "foo@bar.com" login.
HoweverI really recommend using IMAP for Gmail accounts (both free / personal @gmail.com ones and Google Apps ones, there is no difference).
You'd need to add the account again into Aqua. Tap Manual after entering your name / email / password.
The incoming server type should be IMAP (default), the rest is imap.gmail.com + SSL + port 993, outgoing is smtp.gmail.com + SSL + 465. Your login should be "foo@bar.com" for both servers and back on the initial account setup screen.
Now you'll have access to folders, two-way sync for read/unread/starred state, etc.
Once you've added the account into Aqua as IMAP, and verified that it works to your liking, you can delete the POP3 version from Aqua (long press the account / choose from popup).