Apple Mail stops downloading emails at a certain point

Hello,
I have just recently started to use Apple Mail (3.6) and set up two accounts: one POP for hotmail and one IMAP for gmail. While sending mails works fine with both accounts, the hotmail one stops downloading mails from the server at a certain point.
From the approximately 15000 mails on the server, Mail downloads about 3000 (the oldest ones, which I neither need nor want on my computer anyway) and then stops. When I click on receive new mails, it will show the connecting sign as usual. The bar on the left, which indicates how many e-mails remain on the server and how many are currently being downloaded, pops up for a second, telling me that all remaining 12000 e-mails have been downloaded in the same time span - which obviously didn't happen.
I have already tried deleting downloaded mails from my computer, thinking that there might be a limit to the number of mails saved on the desktop. Also I deleted the whole account and set it up again, but the same thing happened at exactly the same point, respectively the same email downloaded. What to do?
Thanks to everyone who can help me out with this!

Yes, these were the e-mails that showed up in the inbox, i.e. they were the chunk of mails that I could download before Apple Mail stopped the downloading at all. I deleted them because I thought it would make space for newer ones to be downloaded.
No, I have not used any other Mail application before. I used to go directly to the hotmail-webpage.
Interestingly, I have deleted the whole account again and set it up anew - which enabled Apple Mail to another round of downloading mails when I did it the last time. This time however, nothing happened: again, the bar on the left appears for a second, telling me that around 12000 mails are on my server and that all have been downloaded in about this second. But they do not show up. It remains a mistery to me, even more so as Mail is obviously able to detect all mails on the server (when I check under Account Information, Emails on Server) but not to download them.

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