I don't know what the problem is but I suspect it has to do with the fact that these files are on an ntfs partition. I have tons of music with accented characters, including a tilde over an n, and none become hidden because of the tilde on a native Linux or UNIX partition. The character isn't the problem except perhaps in ntfs-3g. Thankfully I don't run Windows so I don't have to deal with any of this nonsense.
Do you have an ext2, ext3, xfs, jfs, or reiserfs partition anywhere? Try moving the files to a native *nix partition and see if that fixes the problem.