Since the problem predates Windows 8.1, the odds are that a clean install is the most likely way to solve the issue. There is probably a setting that needs to be changed but what that is up in the air.
For the software that you have paid for, take an inventory and check to see what software you have activation codes for and which you don't. Contact the vendors involved to explain the situation as they may have a record of your transaction even if you do not. They may have a setup where they can provide you with activation codes and/or download links to your software after the reinstall.
Alternatively, here is an article on changing indexing options but these are probably things that you have already tried.
http://windows7themes.net/lets-change-the-indexing-options-in-windows-8.html
If the issue is with you current user account, create a new Administrator account and see if you can rebuild the index as that user.