Initially I'd be trying a larger cap in C51's position, and one that has a low esr, it sounds like the voltage on this cap is dipping low enough for the '34063 not to regulate properly.
Ideally you'd want to calc the value, there are implications on other aspects of the circuit such as inrush, so you might need to beef up the 1n4007 and increase the fuse if your able to do so.
Its also going to affect stability & your compensation network being a voltage control switcher, can you rerrange the power supply to maybe + - 12v ac.