BTW, this has been changed/fixed in the CC version.
For EPUB3 we removed all the DOCTYPE entries from all the files - not just the toc.ncx but all the files in the <spine>.
Did you perhaps miss one of the latter files? Just search with whatever tool you use for DOCTYPE.
Thanks Douglas. I'm using a friend's laptop and his copy of InDesign. He doesn't want to move to CC and I don't want to pay $50 a month for something I might use for a couple of hours.
Maybe you could suggest they offer a $1 an hour plan (like a prepay mobile) for those of us that are infrequent users and may want to tweak a photo, make a banner or create a quick epub from existing documents