Ah, POP3.
POP3 does not specify how messages are ordered by the mail server. Most order them "oldest to newest", but some use the reverse order.
Not an issue for desktop mail apps, which can afford to download 1000's of messages, and nobody bats an eye at disk space or traffic.
In Aqua, please try this:
Add the account one more time
Use Manual setup
On the incoming mail server settings screen, tap "POP3 message order" and choose "Reversed (rare)"
Check and save the account -- and if this works, just long press and delete the old one.
