Hi,
It sounds as though when you're linking the channels they're defaulting to correct stereo panning. That is, a stereo track is hard-panned so that input 1 goes only to stereo-left and input 2 goes to stereo-right. You could also get the same effect if you were to manually pan your channels 9/10 without linking them or else connect your iPad to an actual stereo input such as Tape In.