My scanner always messes up sketches unless I 
scan them a certain way... I adjust the software 
that it scans into (if that makes sense). 
Microsoft PictureIt's Smart Scan option is 
nothing of the kind - it always slaughters my 
sketches with it's "smart contrast correction". 
Something similar might be happening with you, 
even though I assume you have a different type of 
scanner and software. *shrug* Not much, but it 
might help.