Starting late June, I noticed that my Hotmail messages had stopped downloading. I searched and found other MacFreePops users had been experiencing the same problems.
If you are one of them, don't worry any more. There has been a patch made (credit to CDMackie). It doesn't only fix the problem but some other things too.
Unzip the file and stick it in MacFreePops plugin folder.
The file can be found here: http://www.diludovico.org/forum/showthread.php?t=7267&page=10
It's the 5th post by CDMackie.
Check it out.