There were 3 keys remining in the registry. I'm not sure if lingering keys was the issue as I think there was another file Revo identified that was deleted.
This was, most likely, the cause of the problem. To completely remove bitcoin core, you have to uninstall it, remove the whole directory (after you back up the wallet.dat file) then remove all the registry entries it created.
Happy you managed to solve the issue but you didn't need any software to clean the registry. You could have done it manually from regedit (window + r), search for bitcoin then remove the keys.
Also, in case of corrupt block data, it's better to try reindexing and see if it fixes the problem before removing everything and starting from scratch.