Hello Zeus,
I have recently built a WEBENCH design for a customer with these input conditions: 7-80Vin, 5Vout, 6A Iout at 260kHz. I used the LM5116 demo board for it and it worked pretty well. Can you share your board layout here for us to review? Also, please visit the LM5116 applications note which shows scope shots of a normal operating circuit and that's a good reference. http://www.ti.com/general/docs/lit/getliterature.tsp?literatureNumber=snva226c&fileType=pdf
Since your design is only for 1A load, it seems a bit over designed using the LM5116. We have some regulators (LM5576, LM5575, LM5010) can work for your design. I don't want to steer you away from using the LM5116 now but in the future, you should consider the regulators because their switching elements are integrated. They are much simpler to work with.
Lastly, it looks you are using either Altium or Protel, I have the source PCB layout files in Altium and I will share it with you.