I believe there were problems in the Muslim parts of the Phillippines even when we had bases in the Phillippines.
“By 1970, differential access to both land and government resources had produced a profound economic gap between Muslim and Christian communities throughout Mindanao. In 1971 the same Philippine Senate Committee reported that until that year there were no irrigation projects in any municipality in Mindanao where Muslims were a majority (Gowing 1979).”
“As early as 1954 the economic disparities between Philippine Muslims and Christians generated by Christian migration to the Muslim South were already becoming conspicuous.”
http://asiasociety.org/origins-muslim-separatist-movement-philippines
They were beheading monastery monks even way back when, per Filipina that I used to work with a couple decades ago. Didn’t make the news, but was constant issue.