Auto tone always makes a big difference to photos....why?

[primalcarl]

I have a Canon 400d and notice that when I choose 'Auto Tone' in Lightroom it makes my photos considerably lighter. It leaves me wondering which I should trust, my camera or the software. Admittedly images are quite often a little dark, but that happens whether I'm shooting in auto or manual.

How often do you use Auto tone/colour options?