Is either one of the two utilities you use, (OE and web-based email), better at spam control than the other?
If you have set up message rules in OE to remove certain types of spam emails, they may be being deleted as soon as they are downloaded.
If not that, perhaps others here will have better ideas about 'syncing' problems.
On a seemingly random basis, we are finding email messages in netmail/webmail (verizon.net email) that never get picked up by Outlook Express 6 when we download from the verizon server. Running xp SP3 with IE 7;
Any thoughst on a better email app?