I use Outlook Express and in some email accounts I set to leave emails on the server permanently, so they can be downloaded by other computer.
I have no troubles with avast! and this setting.
Hmm, I´m thinking how MS Outlook (not Express) handle this feature. Maybe avast! team could say something about…
MS Outlook handles the email server in the same manner as does OE.
As a matter of fact, it has the check box in the same location under Tools-Accounts-Properties-Advanced.
The mails that don’t get deleted from the server were probably downloaded before you installed avast. When avast Mail Protection Wizard modifies your account (I suppose we are talking about Outlook Express), OE resets its internal counters for that account and forgets its ‘history’. I think that if you delete all mails from your mailbox now, it will then work as before.