That's correct - both paths are stereo. The difference with Input2=Variax is a weaker signal. That can mean nore than a lower volume. For instance, you will be familiar with the fact that turning down the volume on your guitar can also affect the level of dirt/grit/crunch in your tone depending on how your amp's drive/gain is set. The same thing applies here. Setting Input2=Variax instead of Guitar is similar to turning down the volume knob on your guitar.

I guess the tuner thing is like Silverhead said - only Input 1 goes to the tuner.  But that makes me wonder...what are your mixer settings?  Are you panning hard left/right for each Channel?  I prefer to mix my amp tones down to mono and only use stereo effects for any stereo separation, but that's just me.  So I use center pan on both channels for a dual amp tone.  This brings up a whole new ball of wax:

http://line6.com/support/thread/88099

so i took a look at the rest of the patch.  First thing I see that screams red flag is in Channel B you have the Tube Comp set to 0% Threshold.  This is basically compressing the crap out of your tone, which you then feed into a distortion unit.  That's going to kill any dynamics to your playing.  I would actually put the Tube Comp behind the amp, and use Threshold between 30-70% depending on taste.

Another possible no-no is using the Parametric EQ last in the chain.  These effects (Mid-Focus as well) are often subject to clipping on anywhere near a hot input.  You may be able to get similar EQ treatment out of a Studio EQ which is not subject to this problem.  If you keep the Parametric, try putting it right behind the mixer and make sure the levels are low enough so that it doesn't clip.

Curiously, what's in your FX Loop?  And if you have to reduce the level to keep the Parametric from clipping, you may be able to gain it back in the FX Loop's Receive control.