Yeah, I don't put too much stock into the custom tones or the presets.
If it sounds like it's clipping, it probably is. You might be coming in too hot, so you could be clipping the input
Does rolling back the volume a bit on your guitar help? (I know, it doesn't seem righ to do that on high gain tones)
Also try the tube overdrive before a high gain model, keeping the gain dailed down on both.
Line6 does recommend high impedance headphones, although many don't have problems with lower impedance, some do describe them as sounding harsh.