If you use the option "8 - Prevent File Re-check", this should solve this file checking problem.
If everything fails, make sure you create a manual backup of your "pad00000.meta" after each update, and restore it when you see there is a new patch.
This shouldn't be necessary though, but apparently my tool's system is not working 100% of the time.
Still, to not get stuck in the "corrupted files" loop. Simply delete your "version.dat" (but don't restore the backup after that, otherwise you're gonna have to delete this file again), and open the launcher and wait for the file re-check, and it will re-download the pad00000.meta file only.
This was written in the "troubleshooting" part, on the first page.