UPDATE WITH FIX:
After failing to reinstall the update I checked the event viewer for the exact system error message. My error code was System Error 1612 which is a problem with the MSI installer package.
Download the Uninstall Trroubleshooter from the ms support link above and run it to uninstall FFlogs from the registry. Then simply download the latest version of FFlogs and install it through Adobe Air like normal. FFlogs uploader now works perfectly for me, hope my solution helps.