Actually, the files I uploaded were true PDF and were able to be opened by Adobe reader. The issue was interesting. What's causing the error was exactly like the error code described: the binary header was not started with "%PDF". Open the pdf in latest adobe, then save the files as pdf solved the problem.
For those who are interested in checking a file's header on Linux or Mac, open terminal and use "hexdump -C {your file name} | head -n 100". This command will show the first 100 bytes of your file. In my case, my pdf files had some weird dummy header before the "%PDF-" and therefore caused the error from the IRS end. "od -bc {filename} | head" also does the job.
Cheers
