Why L6743D MOSFET driver is not working properly?
Belay the answer below!  Thanks for the clarification of your application. The answer is appropriate for a buck converter.  Your problem is that this chip is designed for the buck converter and not a brushless motor, so you will have to play some tricks if you want to try to make it work.  You would have to use the enable signal to disable one of the drivers for the open phase, leave the low side driver on for the low side phase and perform PWM on the high side using either the enable pin of you want the phase open for PWM, or use the PWM input  if you want to take the high side to ground for PWM.  You still have to follow the rules for a bootstrap capacitor.

Chances are your PWM signal frequency is not high enough, or your bootstrap capacitor is not large enough.  When the low side FET turns on, it pulls down the low side of the boot capacitor charging the capacitor to 12 volts in your case.  Then when it is released its charge pumps up the BOOT input, so it needs enough charge to provide a voltage that will be higher than Vcc so that you can turn on the HS FET.  Remember that to turn on the high side FET, the gate must have a voltage greater than the source, so you must have a voltage on this capacitor greater than 12 volts with respect to ground (greater than the voltage on PHASE). The charge pump can only charge the cap when the PWM transitions occur, so if the transitions are too infrequent (low frequency) and/or if the boot capacitance is too small (not enough charge), you won't be able to maintain your high side voltage and the HS gate will not remain above 12 volts.  It's a little confusing in the data sheet because the low side gate voltage waveform is measured with respect to ground, which is a direct scope reading, but the high side voltage is measured with respect to its source (the PHASE signal), so it won't look like the signal in the timing diagram but will follow PHASE up and down.