The Comelec first tried automation in 1998, based on optical scanners, similar to the technology they are using today.
Ballots for the province of Sulu were re-counted at the Philippine International Convention Center (PICC) due to an error in NPO’s printing procedure. Results in several municipalities in Lanao del Sur were re-counted manually also due to errors in printing of the ballots and procedural errors.
In short, printing problems also resulted in the misalignment of bubbles (as they called the ovals then), forcing the Comelec to recount ballots from Sulu and some towns of Lanao del Sur.
In 2010, the misalignment was caused by the high-speed printing, as the Comelec itself acknowledge in the case of the ultraviolet security mark. This forced the Comelec to revert to a manual method of authenticating each ballot using visual inspection by election inspectors wielding ultraviolet lamps. If the UV marks are misaligned, then the ovals themselves can be misaligned too.
If so, then we might have no choice but to count votes again, ballot by ballot.