I have been working on getting Fetchmail up and running with my ISP email. Everything seems to be working properly, except Fetchmail seems to be deleting my emails instead of downloading them from my ISP email server.

Here is the part of Fetchmail -v that seems to be the problem.

fetchmail: SMTP> MAIL FROM:<Jeremy.Coutts@T-Mobile.com> SIZE=3528
fetchmail: SMTP< 250 2.1.0 <Jeremy.Coutts@T-Mobile.com>... Sender ok
fetchmail: SMTP> RCPT TO:<Jcoutts1@localhost>
fetchmail: SMTP< 250 2.1.5 <Jcoutts1@localhost>... Recipient ok
fetchmail: SMTP> DATA
fetchmail: SMTP< 354 Enter mail, end with "." on a line by itself
#***************************************************fetchmail: SMTP>. (EOM)
fetchmail: SMTP< 250 2.0.0 hA4CLUFx002861 Message accepted for delivery
flushed
fetchmail: POP3> DELE 1




Thanks for the help in advance.

I remember a q/a on the fetchmail FAQ about that it said something like this:
fetchmail only deletes a mail on the server if it's allready downloaded.
So check /var/spool/mail for your missing mails.

I see the mail there. But why is it going there and where should it be going to?

it should be there, but you should install mailx and/or an MTA (mail transfer agent) to read it/transport it to your home directory.
try typing 'mail' on your console, you'll see the mails and after you've read them, they're going to be transported to ~