A current mode boost into a voltage multiplier will have some issues to begin with. The controller assumes that MOSFET current rises linearly during the on-time, and the pulse is terminated once it reaches a certain current as given by the voltage regulation loop. When driving a voltage multiplier off the switching node, the circuit will act as a charge pump when the MOSFET turns on, giving an uncontrolled current pulse that could terminate the on-period prematurely. In your case, the problematic current loop is R2-Q1-C19-D6-C9.
Personally I've had much better success with tapped inductor boost or flyback for converters like this. Standard cheap 1:1 coupled inductors like the SRF0703 work well for tapped inductor boost, with much better efficiency than a simple boost, and cheap off-the-shelf mains flyback transformers like 230 V - 12 V 5 W work very well both for tapped inductor boost and flyback.