Now 76,000 faulty memory cards in machines distributed across the country have to be changed.
"The machines during a test the other day were not able to count the votes correctly,” reports Manila correspondent Girlie Linao.
“What happened was some of the votes were given to a rival candidate. So everything went wrong during the tests and now they’re saying it's because of the faulty memory cards – that these were not configured correctly.”
Officials representing incumbent Gloria Arroyo said Wednesday that there may have to be a delay to ensure the count is credible.
But the election commission insists that the fault can be put right in time.
The 7.2-billion-peso (125-million-euro) computerised system was introduced in an effort to speed up the vote count and reduce potential for cheating.
But Arroyo’s critics accuse her of wanting to hang onto power and local media have speculated that it was designed to fail.
Frontrunner Senator Benigno "Ninoy" Aquino said Wednesday that the glitches have increased his fears about the poll’s credibility and repeated his call for a parallel manual count.
Aquino, who is the son of former president Corazon Aquino, is a fierce critic of Arroyo and has increased his lead over his nearest rivals, millionaire property developer Manuel Villar, and former President Joseph Estrada.
Aquino's campaign received a boost on Wednesday, Linao says.
“A big Christian sect, Iglesia ni Cristo, has endorsed his candidacy to the members. Iglesia ni Cristo has around five million members and these people vote as a bloc.”
Many Filipinos want a stop to the scandals and allegations of corruption that have hounded Arroyo’s administration, Linao says.