This behavior is intentional. We introduced this in K-9 Mail 6.000. The change log entry was:
- Don’t create notifications when manually refreshing the message list
In the past some people remarked that when manually refreshing a folder they can see new messages coming in. In that case notifications are redundant and having to dismiss them is work that could be avoided.
I guess in the future we should only suppress notifications if the message list is visible. And if another app is in the foreground we should generate notifications for new messages.
As a work-around you could swipe down on the folder list in the side drawer. This will refresh all folders that are configured to be checked in that account. Doing so will never suppress any notifications.
You can also open the side drawer, expand the account list, and swipe down on the list of accounts. This will check all accounts (and not suppress any notifications).