Don Beusee - 2006-07-18

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This is by design. It only happens if "apply limit to
message list" is not checked.

Here's what the help file says:
Apply limit to message list:
Enable this if you want YPOPs! to apply the Maximum number
of emails per pass limit to the message list. This has
the affect of hiding any additional emails in the folders
from the email client – as if there is nothing else
there. One reason NOT to do this is that if you tell your
email client not to delete emails from server (possibly
until later), then the email client will think those
emails are not on the server any more. This can have
undesirable side affects, such as duplicate emails, emails
not being removed from Yahoo, etc. If deleting emails
during download, this option is useful to avoid the email
client from displaying an ugly error when the limit is
reached (when there are more new emails than allowed to
download in a single pass). This is also useful for DSL
users, because DSL can do things a little fast and Yahoo
may give error 999 which will lock the user out of their
Yahoo account for an hour.

You can safely ignore the error and don't change the
setting if you are not deleting emails from server during