I use a Focusrite Pro40 and I've experienced similar problems.
If I try recording my acoustic guitar with a condenser mic I need to crank the preamp gain to get a usable signal and it gets noisy.
I have a Roland MMP-2 with spdif out that I use when recording quieter sources.
If you go to the Focusrite FAQ on their website,it seems to be a common question that they don't see as a problem.