Ok so after playing around with some test values I figured out what the problem was.
The values reurned in the RGB columns are premultiplied by alpha.
This is because the premultipliedAlpha flag of the WebGLRenderer is by default set to true.
To fix this behavior, set:
var renderer = new THREE.WebGLRenderer( { premultipliedAlpha : false } );
during construction of the renderer being used.
Also, make sure that when you create the material to be applied to the framebuffer you set its blending to none:
material.blending = 0;