A couple of years ago i did quite a big job scanning a document and converting into word format.
I found that the software which did the conversion from scan to word (I think it was called textbridge) was very sensitive to some of the scanning parameters.
Experiment a bit. Don't scan in colour, make sure it is black/white, not greyscale). Adjest the contrast values to give the best distinction. Don't scan at too high a resolution (Sounds crazy, but try it)