I've been having the SAME problem. Prior to adding an iphone 4 to the mix.
Here is the scenario.
GF, mac, iphone 1, earthlink mail, deleted from server after deleting on either IPHONE and MAIL ON MAC client, after deleting trash. Worked fine.
Now, she has iphone4, setup earthlink pop mail, mail no longer deletes from server, even when using the mail client on the mac.
MOM: Had pc, and iphone 1, earthlink mail. Mail deleted from server after deleting on the iphone 1, and deleting trash AND if she used her pc client to get pop mail, deleted trash, it deleted from server.
Now, I just moved her up to iphone 4, and moved her to a macbook air. Setup the accounts the same, let the iphone 4 SELF CONFIGURE the earthlink pop account. Now, NOTHING deletes from the server, not the mail client on the MACBOOK or the iphone 4, JUST LIKE THE GF devices.
So, WHAT has changed at either earthlink, or is there something that the ihpone 4 self configuration DOES to the server?
Also, how to fix it, become it is untenable as it is