Large folder on external HDD - finder cannot see all files

So I bought a new MBP and I was planning on finally bringing some sense to the horrible, horrible clutter on my externals. Primarily I wanted to properly fill out all the ID3 tags for music (using the so-awesome and auto-tagging Jaikoz.) When I plugged my HDD into my new computer I realized that my music folder (approximately 450 gigs/4000 folders) was only showing about 70 folders. When I checked the info on the folder it remains the correct size and when I return the HDD to my previous computer all of the associated mp3s in iTunes still play properly and are stored in the correct folder according to the info box (though the 70 folders only issue persists.) Needless to say I am freaking out; has anyone encountered this or does anyone have any ideas on how to address this issue?