Based on the error message there may be something wrong with either FDF or PDF. Could you please forward the relevant files and we will take a look?
However, before this could you please check if the following recent builds help with the issue:
32-bit, .NET 1.1-3.5:
http://www.pdftron.com/ID-f94ls2-edm0aqZ/PDFNet.zip
32-bit, .NET 4+:
http://www.pdftron.com/ID-f94ls2-edm0aqZ/PDFNetDotNet4.zip
64-bit, .NET 4+:
http://www.pdftron.com/ID-f94ls2-edm0aqZ/PDFNet64DotNet4.zip