In the VPOP3 settings sometimes, on the user account list the “Inbox Count” is shown as zero, but the “Mailbox Size” is not zero.

This is not a bug, or mistake - the two figures are showing different things.

The “Inbox Count” is showing the number of messages in that user's 'Inbox' The “Mailbox Size” is showing the total size of the messages in that user's entire mailbox.

Users can have other mail folders, other than Inbox. This is most obvious in VPOP3 Enterprise, where all mail folders are stored on the server (if you use IMAP4), but still applies in VPOP3 Basic, where users can create folders in Webmail.

A common situation is that a user logs in to their Webmail and deletes some messages from their Inbox. The Webmail system then moves these messages into the 'Deleted Items' folder. If you do not empty the Deleted Items folder, the messages will no longer be in the Inbox (hence count = zero) but will still be in the Mailbox (hence size <> zero).

If this is an issue, then simply log into the user's Webmail account, and delete the messages from the Deleted Items folder.