Well some times folks will que up for the same file twice, and also in the WinMX 3.54 beta 4 version its pretty easy to share a folder twice by accident. This will make two copies of your files show up in your browse.
If you go to the Library screen and then click on Settings and make sure its not set to share sub folders.
If those settings are ok, and that is not whats going on then by chance would this be mostly for one certain artist or track you notice this with?