If you backed up your saves directly to CD-R and then restored them by copying them back to the hard drive, you need to select those files on the hard drive, right click, select Properties and clear the Read-Only flag. If the files in the save folder are marked Read-Only, the game will crash trying to load the save. That would not cause a problem with Windows, though.
If you zipped the save folders before backing them up to, or used a backup program that writes to an archive of some sort, then you would not have a problem extracting the files from CD-R. Of course if you just moved the saves to a different folder on your hard drive, or something, then they would not have been marked Read-Only, so this wouldn't be relevant.
If you have any more problems with data corruption, you may want to check out your computer for hardware problems. A couple corrupt saves may just be the game, a problem with Windows could just be Windows, but if it continues to happen in multiple programs or starts to get more frequent, there may be a deeper issue.
There are a couple memory testing program you can try; Memtest86
/ MS Windows Memory Diagnostic
Your hard drive manufacturer should have a utility on their web site to check the drive. If you want I can be more specific, or you can invite a geek friend or relative over for supper.
One thing you should do, if you haven't already, is run a ScanDisk (right click on the hard drive in Windows Explorer, select Properties, switch to the Tools tab, and hit the Check Now button in the Error Checking Status section).