Amer,
I've heard of a few people having this issue, but it sounds to me like the following occurred:
-You backed up all courses on your 1.6 site.
-You restored all courses on your 1.8 site.
What works better is if you backup the database and restore that, and then you don't have to do any restores. It's all done at one time. This also keeps all ids the same, keeping image links, resources, etc all intact and ready to go. Just make sure that when you do the restore that you also point the new installation at your moodle data directory!
Hope this helps! Best of luck!!