Received emails are being deleted from Mail but still showing on webmail!!

Hey people! I wonder if anyone can help?
I hope i'm not missing something really easy here. A couple of weeks ago i thought i was deleting emails from my inbox and then from my trash with no problems and then imagine my surprise when i get a message saying that my mailbox is almost full and i can't receive any messages.
I promptly logged on to a webmail site and entered my details and was greeted with every single email i have received since i got my new mac!! I have rebuilt mailboxes to no real effect and was just wondering if anyone can offer a solution? After all i don't really want to keep having to log on to webmail to delete all my items every few weeks.
Just to add, my email account is with BT and is NOT a .mac account!
I look forward to anyone helping me please?? I'll wash your car in return or something
iMac G5 Core Duo 2GHz Intel   Mac OS X (10.4.5)   1.07GHz G4 iBook + Dual 2GHz G5 both running 10.3.9

Is the account a POP type account?
If so, go to Mail > Preferences > Accounts and under the Advanced tab for the account preferences, is "Remove copy from server" selected? If yes, what is the setting below?
I use "Right Away" for my POP accounts.

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