Due to my unwillingness to sit around for hours waiting for my renders to be finished and hitting a different checkbox each time, I stumbled upon a new script:
hou.cd("/wherever/your/node/is")
hou.pwd().cook( force = True, frame_range = (startFrame,endFrame,1))
hou.pwd().cook( force = True, frame_range = (startFrame,endFrame,1))
When placed on the matra ROP on the pre-frame script, this forces the material to re-cook each frame, allowing the checkboxes to be re-evaluated and the correct pretty picture to be outputted.