LT1172 3 V to 300 V converter issues
so I wound 19 turns on the primary (48uH) and took a punt on 200 turns
for the secondary which worked perfectly as mentioned.

OK with 300 volts on the output, the flyback voltage on the primary will be 300 volts * 19/200 = 28.5 volts.
But, you have a 25 volt Zener clamping that to probably around 26 volts and that seems likely to be a problem. Transformer action still holds in a flyback design. If the secondary peak voltage is 300 volts, that will be see as a flyback on the primary divided by the turns ratio reversed.
I'm not saying that's your one and only problem but it strikes me as being significant to your issues. If you have a 10:1 step up transformer and your output voltage is nominally 300 volts then, your Zener flyback catcher needs to be in excess of 30 volts (simple math).