Improving recognition results
Taking 10 minutes to go through HELP/TUTORIAL and lesson 6 will greatly improve the recognition of poor original scores. In particular you need to scan in greyscale and experiment with the contrast and brightness sliders. Under the PAGE menu there are filters to remove the specific problems of shadow, speckles and areas that need erasing
Improving errors in assigning instruments to the score
Look at HELP/TUTORIAL and lesson 5. When you scan scores with many parts that come and go, capella-scan can sometimes not follow a part through the score. When this happens it will assume it is a new part coming in. Lesson 5 gives examples of this and how they can be corrected.