Simple step-up transformer not working as expected
It sounds to me like you may have an average DC voltage across the transformer, which means you will saturate the core, or drop most of the voltage across your power resistor in series.

This would be the case if you were simply switching the primary with one end tied to your supply and the other to a FET to ground.  If you are doing something different than that please add a schematic to show what it is and we can supply a better answer.

Try driving it with a bridge, to allow the flux to reset or coupling to the primary with a capacitor.