If you have a gap in synced messages, see very old messages that would not normally be synced or see very few of your new messages very likely your mail server's message timestamps are no longer correct. To return correct order to your messages, adjust the following option:
Settings > Manage accounts > your e-mail > IMAP Options > Which message date/time to download > Date/time sent (from the message header)
This changes how Aqua Mail sorts your mail and instead of monitoring the server timestamps it will choose the message sent date from its headers.