Hi Steffen,
Cin is so high because WEBENCH calculates conservatively under the assumption of a slow input source. It sizes Cin to be able to handle providing the full input current for one switching cycle with a 5% voltage ripple. After you get the rest of the circuit working you may be able to reduce this size based on your application and your input source ( i.e. if you will have a large load transient, will the source be able to provide the needed current quick enough? Most likely the majority of this current will need to come form the input cap)
The sense resistor is small because the IC sums its internal ramp voltage with the current sense before comparing to the Current sense voltage limit. This means at high duty cycles you will not need as much as you expect for Rsense. (Please see Datasheet pg. 16 for more details)
The second picture you attached shows that the part is still switching at the expected frequency, but that every other pulse is just on for a minimum amount of time. Something is unstable and it is most likely related to the physical layout of the board.
My first thought is that you should connect the Csense to the other side of Rs1 and directly to the Isense pin. This will help filter any noise that is happening here causing the second pulse to turn off the switching cycle.
If this does not help we will need to take a look at the overall board layout.
Best regards,
Tommy Jewell