Were the libraries ever renamed? The library consists of a file and a folder. If your library were called My References you would have a file called “My References.ENL” and a folder called “My References.DATA.” The names of the file and folder must match exactly.
Where on the hard drive are your libraries located? If the libraries are in the Program Files or Program Files (X86) folder you will have problems with the library. This is a restricted area in the newer versions of Windows.
Are the libraries located in a folder that is set to be synchronized or backed up? Synchronization or backup programs can sometimes modify the contents of the RDB folder, which is inside the DATA folder of the library and cause the library to become corrupt.