By default, VPOP3 will treat INCOMING mail from local email addresses as suspicious, because this is not normal.
Normally, mail from local email addresses will be sent by the users through the VPOP3 mail server so will not be filtered by the spam filter.
However, if you have local mail coming in from across the Internet for some reason, then VPOP3 will see that as suspicious because it is a very common spam trick to send spam from the same domain as the recipient, in the hope that the sender's email address will be whitelisted so the spam will come through the spam filter.
Solutions
Send mail through VPOP3
The best solution is to have all the users for your email domain send their email messages through your VPOP3 server. To do this, simply configure their email clients so that the SMTP server is configured as the VPOP3 mail server, with the appropriate login details.
For instance (in Mozilla Thunderbird):
Force VPOP3 to whitelist local email addresses
If sending all mail through VPOP3 is not possible for some reason, then you can force VPOP3 to allow whitelisting of local email addresses. To do this, go to Settings -> Spam filter -> General -> Script Configuration, and set 'CheckLocalWhitelist' to '1'. Then, add the local email addresses to the spam filter whitelist. Note that if you do this, then, when spammers forge the sender's email address to be one in the local email domain, then the spam filter cannot block it because it cannot tell the difference between an incoming mail from one of your users, and an incoming mail from a spammer.