Hi,
Yes, I think there is a bug here, at least I can confirm from our test servers. I do not recommend turning on that option, it is not very efficient for such large databses, and will not resolve the issue.
This may be only possible to resolve by directly editing the index table engine file. I tried to open the plugin editor, but the account does not have privileges. Can you please try this:
1. Make a full site backup just in case
2. Open up the wp-content/plugins/ajax-search-pro/includes/classes/etc/indextable.class.php file on your server
3. Replace it’s contents ith this
4. First, only test on one post – Open the post editor screen for a post, change it to password protected and save it.
5. The post should update in the index automatically during saving, so now if you try to search it, it should not show up
6. If that actually works, then re-create the index.