I was trying to use the "Cloning" features to calculate restriction fragment sizes. I used "Digest into Fragments" that showed one site for Eco RI and Xho I in a plasmid, and I can see those sites on the circular view of the plasmid. However, when I use "Construct Molecule" the program reports "Xho I site not found" even though I can find this site in the sequence view. That site is not reported in the "Digest into Fragments" report, although it is listed as having one site earlier.

Thank for the additional info. We are still fixing this Windows 8 issues...