One way to rebuild system files is the System File Checker. You might try running that to see if it can see any problems. But, I have seen situations where if the backup files are also corrupted, it won't help. Open an administrative command window and type:
SFC /scannow
I suppose running a hard drive check could help.
Have you tried removing locations from the indexing list, which might be different from rebuilding the index. Perhaps that are corrupted files in your search area and causing a problem. Or you may be attempting to index/search a location that is not available, such as a flash drive or other external source, maybe even something on your network. Possibly rebuilding the index would have covered these possibilities...