Sounds like all plugin files including BPS Pro plugin files were quarantined due to some problem. Do the steps below to be able to use the XTF tool. I assume that you will see that files have been quarantined when looking at Total Files: X under the Current Status column. You can restore all files in Quarantine using the XTF form. Also reinstall the Kleo theme by just manually copying new files/folders to the Kleo theme folder while AutoRestore is turned off and then run the Setup Wizard again.
http://forum.ait-pro.com/forums/topic/xternal-tools-xtf-guide/
Note: XTF is a stand-alone tool. If BPS Pro plugin files are quarantined due to some issue/problem and you want to reinstall BPS Pro using XTF do the steps below:
1. Unzip the bulletproof-security.zip file on your computer.
2. Upload the xternal.php file from the BPS zip file to this BPS plugin folder: /bulletproof-security/admin/xternal/xternal.php.
3. Go to the Xternal Tools page in your Browser: example.com/wp-content/plugins/bulletproof-security/admin/xternal/xternal.php.
4. Select the Turn Off|Deactivate AutoRestore|Quarantine (ARQ) XTF Form option and click the Submit Xternal Tools Form button.
5. Use the Reinstall BPS Pro plugin files tool to reinstall BPS plugin files.