I have a program that downloads mails from my Gmail, i have selected the radio button : Enable POP for all mail (even mail that\'s already been downloaded)
You don't need to re enable the radio button, when a pop client downloads the mail, it cant be view by other pop clients. How outlook does this is by using the recent mode.
Try this its not all your mail but the last 30 days.
Just Add recent: to your username e.g recent:Me@gmail.com.
Recent mode fetches the last 30 days of mail, regardless of whether it's been sent to another POP1 client already.
Link to back it up.
http://support.google.com/mail/bin/answer.py?hl=en&answer=47948