Thanks for your post.
This sounds unusual. I've just tried it here, with a commandline of:
sqlcompare /db1:<db> /db2:<db> /scriptfile:c:\\somefolder\\somescript.sql
This worked fine, and the file was generated. Are you working with any other switches that may somehow be conflicting? The full command may help. Also, what version are you using? If your scriptfile already exists, you may need to add on the /force option to overwrite it; but I think the same would be true with the /sync option set.