hmm, and how many analog channels are enabled in the project settings? if it's 8 (as per the default), then it may actually be that it is behaving properly: the large ones will be the ones that are looped back and the small ones are the ones that are disconnected.
You can try to replace the line
scope.log(context->analogIn + n * context->analogInChannels);
for(unsigned int ch = 0; ch < context->analogInChannels; ++ch)
logs[ch] = analogRead(context, n, ch) + 0.5f - ch / (float)context->analogInChannels;
This will stagger the channels in the plot so that they are not overlapping, and you can see each individual one. Alternatively you can move them around manually with the sliders in the scope controls.