I am not quite clear on what you are doing, are you trying to switch the LT3741 on/off at some frequency (40hz and above) to flash the LEDs?
If so, I think you are using the wrong approach.
Having looked at the datasheet, there is no specification for switching to output on/off.
If you look at the 20A LED driver circuit in the datasheet, there is a 680uF capacitor on the output, there is no way that you are going to charge/discharge this at a fast rate.
I think you need to use the LT3741 to provide the current, and a separate switching circuit such as a transistor or MOSFET to switch the current in the LED.
JimB