I wrangled with this for days, trying to figure out why when I sent the FDF using response.write, it just wouldn't display in Reader. I tried sending both hand-crafted FDF and installing the FDF toolkit to create the FDF response. I was able to create valid FDF, as I was able to open locally in Reader and have the pop-up display correctly but I couldn't get it to work for the life of me sending FDF from my ASP.NET page.
Then inspiration struck. In one of my attempts to send the FDF, I stored the FDF in a file and tried to use a streamreader to pump it into the response. After many unsuccessful attempts to use response.write, on a whim I tried response.redirect to the saved fdf file and it worked. I had previously added fdf as a registered MIME extension for my web site, with application/vnd.fdf as the MIME type. Now the user receives the pop-up after successful submission. The simple solution, in C#, looks like this:
Page.Response.Redirect("success.fdf");