Can you check that the field "Interchange Control Number" is correctly set in the json you are passing to the import?
The Sample data Celigo shows in the top right for EDI parsers isn't the actual mock-data it is receiving from any previous steps, it's a separate example that is stored on the import.
I've done that as best as I'm aware of, and I keep getting the same result. I'm just confused as to where it's getting the zeros from. If it's not passing the data from the flow, then it should be a blank string.
This is just a theory, but the EDI Generator V2 / EDI Profile feature sources the X12 header data from the EDI Profile. The profile also contains the next value of the ICN. It could be that when the generator is creating the ISA envelope the document itself isn't loaded yet, just the edi profile, and thats why the handlebar doesn't work. Then the generator pads the ICN with zeros to make it the mandatory 9 chars long.
Edit: could you try if {{0.[Interchange Control Number]}} works? Just a wild thought.