Driving high side MOSFET problem
Yes, the 1K gate-to-source resistor is creating your problem. The good news is, you don't need it. A gate-to-source resistor is needed if your MOSFET cannot be actively driven off when it is needed to be, but that is not the case with the IR2101. You will often see a gate-to-source resistor used when a MOSFET gate is connected to a microcontroller to force the MOSFET off until the microcontroller can initialize the pin as an output.

Here is the datasheet for IR2101. And here is the Functional Block Diagram (from the datasheet):

 

As you can see from the functional block diagram, the gate drive outputs HO and LO are actively driven both high and low so the 1K ohm resistor is not needed.

The problem that you are seeing is that the bootstrap capacitor is being discharged through the 1K ohm resistor (in series with the 100 ohm resistor). From looking at the decay rate on your waveform, it looks as though that waveform was captured with only the 330nF capacitor in place (using the formula T=RC to get the time-constant).