Hi Paul. When searching MS's knowledge base I came across this. It refers to IE8, but probably will do the trick for IE9, too. I fired up my PC (Win7 / IE9) and did a test run, experiencing no complications afterwards. When starting IE9 after a reboot, the keys will be created again automatically.
Just be careful when using regedit.
http://answers.microsoft.com/en-us/ie/f ... 3991fe90ce
There is a registry edit you can use to try and correct this if you are comfortable with working with the registry. Before making any changes in the registry I would strongly recommend backing it up first so the changes can be undone should you need to. Here is the change to make:
1. Go to the following branch:
2. Delete all the keys under Favorites tree
3. Delete also the value "Order" on Favorites key
4. Reboot Windows
5. Try to Organize Favorites again
Modifying REGISTRY settings incorrectly can cause serious problems that may prevent your computer from booting properly. Microsoft cannot guarantee that any problems resulting from the configuring of REGISTRY settings can be solved. Modifications of these settings are at your own risk