So to solve it I went around and looked at ~/Library/Mail. I found that in the HTTPMail account folder there was a Junk.mbox and a Junk Mail.mbox file. Therefore I did the following:
cd ~/Library/Mail/HTTPMail-username@hotmail.com rm Junk\ Mail.mbox ln -s Junk.mbox Junk\ Mail.mboxReplace username with your hotmail username. This makes the Junk Mail.mbox file point at the Junk folder. This will mean that when you run Mail.app, the files will end up in Junk.mbox. However, it thinks that it's in Junk Mail.mbox, so it still places them in the separate folder. However, after you re-run Mail, the junk is in the proper junk mailbox.

