I saw this first time live last week:

My colleague's 6 months old 16 GB version has flaking in USB-cover, it has been mostly sitting on the table unused minus calls of course, and has been always in very dry conditions. It's a work phone in a very well ventilated building. I haven't checked yet whether it is made in China or Finland, and I suspect it wouldn't matter since it is USB-cover that has the issue currently.

My 7 months old 64 GB version made in Finland kind of shows some level of flaking after over 7 month's usage. This unit was bought from Nokia flag store in Helsinki the very launch date of N9 in Finland.
It has been both in and out of silicon cover with high humidity at times. I have some dents on it, and I scratched one dent hard with my fingernail to see if anything comes off.
It looks like there is a very thin paint layer on chassis, but it does not have that weird grey color to it like my colleague's phone has. Beneath extremely thin layer of paint it is just black plastic and no grey paint. The bits I'm able to scrape off fall so small, that I can't tell whether any whitish coming off is from my fingernail of actual paint.

But in short; it looks like both black 64 GB and 16 GB versions of N9 have been painted.