Are those mailboxes on gmail?
I’m having a similar problem with a customer and he’s got maIlboxes on gmail or is mail management on gmail servers even with a different domain?
The problem seems to be gmail (who would have thought?).
It can happen that rspamd rejects the email just downloaded with a soft-fail (maybe because it’s busy to so other things).
At that point getmail is instructed not to delete the mail and not to mark it as downloaded so that it can be downloaded at the next round.
Gmail, who is an asshole, thinks instead that the email has already been downloaded and he doesn’t propose it again for the download so that email seems to be “lost”.
To avoid all this, in the pop3 connector, in the “username” field, try adding “recent:” before the username.
For example:
if in the POP3 connector your username is
xyz@gmail.com
replace it with
recent:xyz@gmail.com
Also read here for more configurations on gmail: