So i found this topic and in it it mentions that fpp.setNumSamples(numSamples); causes issues.
Sure enough if I remove that code it works, but is obviously aliased.
However what is not so obvious is this (bear with me): When the scene first loads (with my original code) it works up until the window loses focus. This code contains the call to fpp.setNumSamples(numSamples) even if I force it to set num samples to 4 then the FilterPostProcessor is still aliased, the scene is anti-aliased in the manner I expected, but still broken when the window loses focus.
UPDATE
I get the same problem exactly repeated if I use a different filter instead; I used RadialBlurFilter.