I've also had problems with some pdfs not being recognized by my kobo.
I suspect the problem was that the pdf was encrypted in some way the kobo doesn't support.
Since the book never showed up on the kobo after I copied it over, I kind of forgot about it and never investigated.
So, I just copied the original document to my kobo. I then converted it with calibre's epub-epub, and converted it with ghostscript pdfwrite with -dCompatibilityLevel=1.4
I noticed that calibre's conversion log had this in it:
Code:
Document has copy-protection bit set.
Both of the conversions were recognized, the original was not.
I've used the compatibility level conversion before with some pdfs that were recognized on the kobo but some graphical elements were missing in diagrams.
For this particular document, the calibre pdf conversion scrambled the document a bit. I'm not sure if I like or dislike how it scrambled it.

I might have to play with that more on other documents that have been problematic.
edit: Not surprisingly, the pdf->epub conversion looks about the same as the pdf->pdf conversion, scrambled in pretty much exactly the same way.