In version 4.0.0.0 the Form.FillField method adds a new Node to the Xml structure instead of setting the existing one. In version 3.8.0.1 the Form.FillField method sets the existing field properly.
I have attached a sample project demonstrating this behavior.
I have reproduced the problem at my end and logged it as PDFKITNET-13311 in our issue tracking system. Our team will look into this issue and you’ll be updated via this forum thread once the issue is resolved.