The problem is this line:
Response.OutputStream.Write(MS.GetBuffer(), 0, MS.GetBuffer().Length)
The GetBuffer method returns the entire internal buffer which is larger that the actual content. The bad PDF has about 10kb of garbage content at the end (bytes of zero), the good PDF has only a few garbage bytes. Use the ToArray() method of the memory stream to get the PDF file and the problem will be fixed. You will also get smaller files.
byte[] pdf = MS.ToArray();
Response.OutputStream.Write(pdf, 0, pdf.Length);
Also set the "Content-Length" with the length of the pdf array.
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