Some brands of tuners (Intellituners didn't work well for me) have troubles with some ranges outside the normal guitar range. If you can get the low string of the pair tuned, you can fret it at the 12th fret and match the high string of the pair to that.
I have used differenrt tuners and I tune my 6 string the same way. It is just g c e a. The paired strings I tune one at a time but they both register c or a on my tuner. The string's dimension automatically take care of the octave part.
So basically you should tune it g c c e a a.
If that doesn't help I'll try to get a video up tuning my 6 string for you.
The octaved strings are usually C and A. Another string option is g Cc E AA. Never had any problems tuning with a clip on. The 12th fret harmonic work well.