I have never had problems with making or restoring library backups. I suppose that something on your PC prevented MC from being able to properly copy the library data files (*.jmd) during the backup process.
*A library backup zip file just contains the .jmd files from the library data folder. You can effectively do the same by copying the .jmd files to some other place when MC is not running.
A "restore" simply replaces the current .jmd files in the library data folder with the files from the backup zip archive. You could also manually replace the .jmd files in the library data folder with another set of older unzipped .jmd files (naturally MC should not be running during this).
There is a difference though. During a library restore MC deletes the thumbnails file (thus forces MC to rebuild them) because the current file would not be in synch with the older library data. You can do also this manually in Options > Tree & View > Thumbnails.
Edit
* ... or if the zip file is fine then something may prevent MC from restoring the files.
You could try another library data folder location instead of the default location in the "C:\Documents and Settings\[your username]\Application Data\J River\Media Center 11... " path. Try something simple and totally unrestricted. (I have my main library in "C:\XYZ\".)
Edit 2
when MC is not running
- read this as: "when the main MC program or the separately started Media Server program is not running"