The situation is murky. Naomi Klein, in a rare attempt to explore the murk, examines the claims of the mutineers in The Nation , and offers a few a guesses about what the truth might be:

"In the six months since, while all eyes have been on Iraq, there has been a spike in terrorist bombings in [the southern island of] Mindanao. Now, post-mutiny, the question is: Who did it? The government blames the Moro Islamic Liberation Front [MILF]. The mutinous soldiers point the finger back at the military and the government, claiming that by inflating the terrorist threat, they are rebuilding the justification for more U.S. aid and intervention."

So is the Bush administration being taken for a ride by a government that is fueling terror to reap the benefits of being an ally in the war on terrorism? It's a question too few reporters are asking. The Economist reports that Muslim separatist guerrillas have acknowledged that they buy weapons from the armed forces. But the picture is complicated and politicized, The Economist notes:

The idea that [President] Arroyo plans to declare martial law so that she can remain in office is tortuous. She would have a reasonable chance of winning the next presidential election, which is due next year. But Mrs. Arroyo has said she has no wish to run. The notion that opposition politicians instigated the rebellion is based on shaky evidence. Still, the mutineers had expensive radios that were not military issue, suggesting that the rebellion may have been financed by outsiders.

...

Filipinos, beset by conspiracy theories, are in danger of overlooking one obvious explanation of the mutiny: that young, idealistic but immature officers, upset by shortcomings in the institution they serve, decided simply to protest in a manner that they calculated, correctly, would get the attention of the nation.

In a fascinating three-part story, the island's newspaper, MindaNews, investigates the story of Michael Meiring, an American who was nearly killed when explosives he owned went off in his hotel room in Manila. Some in the country have accused him of being a CIA agent who assisted terrorists in order to justify a U.S. military deployment or the establishment of a military base in the archipelago.

Klein recaps:

"These suspicions stem from a bizarre incident on May 16, 2002, in Davao. Michael Meiring, a US citizen, allegedly detonated explosives in his hotel room, injuring himself badly. While recovering in the hospital, Meiring was whisked away by two men, who witnesses say identified themselves as FBI agents, and flown to the United States. Local officials have demanded that Meiring return to face charges, to little effect. BusinessWorld, a leading Philippine newspaper, has published articles openly accusing Meiring of being a CIA agent involved in covert operations to justify the stationing of American troops and bases in Mindanao.'"