Mail fails to erase messages on POP server upon download

My mail (ie tiget mail) is set to delete messages immedaitely upon downloading them from the POP server. Yet, when I go into the web interface from my provider, I can see that the messages are still there, read, but not deleted.
This started about 2 weeks ago, wihtout any changes in my set up.
Any ideas ?
Using latest OS update on Powerbook G4. Service provider is afmu.com.

I did try Thunderbird at your suggestions.
-1- Thunderbird DOES clean up the mailbox on the server after downloading the messages form the server, so it looks like we have some Apple mail problem indeed.
-2- I tried to install T bird properly, and Thunderbird was unable to import / find the settings and mailboxes from Apple mail ( had to create the accounts form scratch) . Does this mean some sort of setting file for apple mail is corrupted on not in the right location ? Which settings file(s) does mail use and where do they live ?
-3- unfortunately, I can not stay with Thunderbird as I use Spamsieve as a junk filter and they do not support Thunderbird..

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