I have been scanning my old photos and using the "seperate scanned photos" app in PSE5. Some times it does a great job but more then 1/2 the time it does not see the division area between photos. I seperate the photos by 1/8 - 1/4 inch, big blue skies usually are seperated from the photo as a narrow strip. Are there any tricks or rules to make it work ?
The scanning software is likely looking for a straight edge with high contrast to mark the separations between images. If your sky is not much different in contrast between the white background on the upper lid of the scanner cover, it likely has a problem in edge location. Try laying a dark-colored piece of paper over your images before closing the scanner lid to see if that helps.
Vicki