I ran into this problem as well. It stumped me last year, and I had to reluctantly print and mail my taxes. This post helped me figure it out, but here's how I did it.
For me, it was also due to 1099s that Turbo Tax asked me to upload. I went through each entry in Turbo Tax by clicking Edit and then opened each PDF that I had uploaded locally on my computer in a text editor (TextEdit on a Mac). Most of them had %PDF-1.3 or %PDF-1.5 as the first line of the file, which I believe is what the IRS is checking for to see that the file is a valid PDF file. Then I found one file that had the following at the beginning of the file:
--MIMEBoundaryurn_uuid_[phone number removed][phone number removed]
--MIMEBoundaryurn_uuid_[phone number removed][phone number removed]
Content-Type: application/pdf
Which was the problematic file, which happened to be from Northwestern Mutual. So I opened in the Preview app on my Mac and re-saved it (File > Export as PDF). You should be able to do an equivalent of this on Windows with Adobe Acrobat by printing to PDF or doing a Save As (not sure, but I'm sure there's a way). Then I verified that the new file started with %PDF-1.x, and then deleted the file in TurboTax and re-uploaded the fixed one. That did the trick! Hopefully that's helpful to someone who's running into this same problem.
TurboTax folks - it would be nice if TurboTax verified the validity of PDF files just like the IRS does, so users don't get into this strange state, or even repaired the files for us.
