Yet another forum thread that's saved my bacon. I've been absolutely head-deskingly stumped at the weirdness of the GPIO on my Omega2+. Pins 0 and 1 seemed to work, but not a single other pin.
It turns out that a combination of this exact problem- woefully incorrect labelling- and the SPI being (as far as I can tell) baked into the kernel and permanently glommed onto the SPI pins (incorrectly labelled 6,7,8,12 on this board) totally explain my confusion.
I've had to use the Omega2 pinout, and manually trace the routes between socket and header to figure out what's going on. Argh!
I wish I had the time to knock up an Omega2 version of my Pi Pinout website: http://pinout.xyz/