Library deleting

System:
Toshiba Satellite A660-135 laptop
Intel Core i3 M380 2.53GHz
4 GB Memory
450 GB Hard Drive
OS: Windows 7 64 bit

Description:
I have a large amount of music on an external hard drive. I have set my wmp library folder as the folder on the ehd that contains all the folders of music and also one folder on my comp that I download stuff to before transferring it to the ehd. I opened up wmp and loaded all that music (I'm talking like 12,000 files) and I can listen to it and works great. I close wmp and then open it again later and the majority of the music has been removed from the library. The folders are still set in the Manage Library window but there are only a handful (about 30 completely random files) still in the list. I can still play all the files directly from their containing folders and all my playlists still show and will play all the right tracks, even if they aren't in my library list, but the full list is gone. If I try deleting the remaining files from my library, not my computer, they don't budge. I have to try several times to remove the folders and then reinstate them to get the program to refresh the library to re-add all 12,000 files all over again. I have been through this process at least 5 times now, this is getting ridiculous. How do I fix this?

Woops, posted this in the wrong forum. Don't know how to delete it here. :P