in a nutshell, scanning in color yields better results because the range of possible colors is greater than the range of possible grays (which is really all B&W is). you're comparing something like millions of colors to 256 grays (or something like that), so when you scan in B&W you're actually throwing away a bunch of information/detail in your image b/c there isn't a value to represent it.
when you scan in color, you scan the widest possible range of tones from your image, which means that you keep more detail in the image. then, do all your cropping, cleaning, sharpening, etc. before you convert to B&W - which is a whole different story b/c there are many ways to do this conversion...
when you were playing with these initially, can you describe your efforts a little bit more - especially how you chose the levels and contrast?
and is your monitor calibrated?