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I will be happy to assist you with your issue. The problem you are describing typically happens when a specific file in the library is moved to a different directory or the file is renamed for some reason. You see, when you create a playlist whether it is based on a library folder or if it is individual files that you added manually, Windows Media Player just creates a text entry in a list that includes the location and name of the file. As a result if you remove a file from its directory outside of WMP, and then open up the playlist, the program will not be able to find the file. It will put a red X next to it, and then give you an error if you try to play it. Then it will remove the entry from the list.
It is possible that this is what happened to your files. There are other options, but they are far less likely. So can you tell me, is this possible? Were some file placed in a different directory, renamed, or otherwise re-organized? If so, it would account for your entire problem. If not, let me know and we will move to the next step in resolving the problem.