I bet that your problem is that your pdf is the NEWEST flavour of them (256-bit AES protected, even if only for certain functions). These pdfs cannot be opened by Kobo, (and neither by Calibre BTW). In older FW versions they even crashed the device. Since 3.12, they just give a
wrong error message about DRM protection.
You can find the whole story in
this thread (which started about a performance drop with other pdfs). If you want to summarize, just jump to
this post and continue reading from it.