Imagine the signal is like a river, and on your clean channel running at 2 you've got a small trickle. Loads of room in the river to add more water (hence the boost works).
On your gain channel, the nature of the gain means the river is pretty full (the signal is clipping). You've only got a bit more water you can add, hence the boost doesn't work as well - you're just overdriving the circuit and causing waves, rather than filling the river up above its capacity.
Can you use a boost in the loop at all, as this may give a better result?
Failing that, you're stuck with the problems LOTS of us have :(